diff --git a/docs/design/plugin_system.md b/docs/design/plugin_system.md
index 3485c40c36811..b0ca2dad23d5b 100644
--- a/docs/design/plugin_system.md
+++ b/docs/design/plugin_system.md
@@ -152,5 +152,5 @@ The interface for the model/module may change during vLLM's development. If you
 ## Deprecation announcement
 
 !!! warning "Deprecations"
-    - `use_v1` parameter in `Platform.get_attn_backend_cls` is deprecated. It will be removed in v0.13.0 or v1.0.0.
-    - `_Backend` in `vllm.attention` is deprecated. It will be removed in v0.13.0 or v1.0.0. Please use `vllm.attention.backends.registry.register_backend` to add new attention backend to `AttentionBackendEnum` instead.
+    - `use_v1` parameter in `Platform.get_attn_backend_cls` is deprecated. It has been removed in v0.13.0.
+    - `_Backend` in `vllm.attention` is deprecated. It has been removed in v0.13.0. Please use `vllm.attention.backends.registry.register_backend` to add new attention backend to `AttentionBackendEnum` instead.
diff --git a/tests/compile/test_config.py b/tests/compile/test_config.py
index 0e91cf525411e..04bb56ecb6470 100644
--- a/tests/compile/test_config.py
+++ b/tests/compile/test_config.py
@@ -1,7 +1,6 @@
 # SPDX-License-Identifier: Apache-2.0
 # SPDX-FileCopyrightText: Copyright contributors to the vLLM project
 import copy
-import logging
 from contextlib import nullcontext
 from unittest.mock import patch
 
@@ -13,7 +12,6 @@ from vllm.compilation.fix_functionalization import FixFunctionalizationPass
 from vllm.config import CompilationConfig, CUDAGraphMode, ParallelConfig, VllmConfig
 from vllm.config.compilation import CompilationMode, PassConfig
 from vllm.engine.arg_utils import EngineArgs
-from vllm.logger import _print_warning_once
 from vllm.platforms import current_platform
 from vllm.utils.torch_utils import _is_torch_equal_or_newer
 
@@ -290,7 +288,7 @@ def test_moe_splitting_ops_deepep_ht_attn_fusion_no_inductor():
         ),
         compilation_config=CompilationConfig(
             mode=CompilationMode.VLLM_COMPILE,
-            pass_config={"enable_attn_fusion": True, "enable_noop": True},
+            pass_config={"fuse_attn_quant": True, "eliminate_noops": True},
             custom_ops=["+quant_fp8"],
             cudagraph_mode=CUDAGraphMode.PIECEWISE,
         ),
@@ -442,62 +440,3 @@ def test_cudagraph_sizes_post_init(
             vllm_config.compilation_config.max_cudagraph_capture_size
             == expected_max_size
         )
-
-
-def test_pass_config_deprecation(caplog_vllm):
-    caplog_vllm.set_level(logging.WARNING)
-
-    # Clear cache to ensure warnings are re-issued
-    _print_warning_once.cache_clear()
-
-    # Test enable_fusion -> fuse_norm_quant, fuse_act_quant
-    caplog_vllm.clear()
-    config = PassConfig(enable_fusion=True)
-    assert "enable_fusion is deprecated" in caplog_vllm.text
-    assert config.fuse_norm_quant is True
-    assert config.fuse_act_quant is True
-    assert config.enable_fusion is True
-
-    # Test enable_attn_fusion -> fuse_attn_quant
-    caplog_vllm.clear()
-    config = PassConfig(enable_attn_fusion=True)
-    assert "enable_attn_fusion is deprecated" in caplog_vllm.text
-    assert config.fuse_attn_quant is True
-    assert config.enable_attn_fusion is True
-
-    # Test enable_noop -> eliminate_noops
-    caplog_vllm.clear()
-    config = PassConfig(enable_noop=True)
-    assert "enable_noop is deprecated" in caplog_vllm.text
-    assert config.eliminate_noops is True
-    assert config.enable_noop is True
-
-    # Test enable_sequence_parallelism -> enable_sp
-    caplog_vllm.clear()
-    config = PassConfig(enable_sequence_parallelism=True)
-    assert "enable_sequence_parallelism is deprecated" in caplog_vllm.text
-    assert config.enable_sp is True
-    assert config.enable_sequence_parallelism is True
-
-    # Test enable_async_tp -> fuse_gemm_comms
-    caplog_vllm.clear()
-    config = PassConfig(enable_async_tp=True)
-    assert "enable_async_tp is deprecated" in caplog_vllm.text
-    assert config.fuse_gemm_comms is True
-    assert config.enable_async_tp is True
-
-    # Test enable_fi_allreduce_fusion -> fuse_allreduce_rms
-    caplog_vllm.clear()
-    config = PassConfig(enable_fi_allreduce_fusion=True)
-    assert "enable_fi_allreduce_fusion is deprecated" in caplog_vllm.text
-    assert config.fuse_allreduce_rms is True
-    assert config.enable_fi_allreduce_fusion is True
-
-    # Test hash consistency
-    config_old = PassConfig(enable_fusion=True)
-    config_new = PassConfig(fuse_norm_quant=True, fuse_act_quant=True)
-    assert config_old.compute_hash() == config_new.compute_hash()
-
-    config_old = PassConfig(enable_async_tp=True)
-    config_new = PassConfig(fuse_gemm_comms=True)
-    assert config_old.compute_hash() == config_new.compute_hash()
diff --git a/tests/kernels/moe/test_ocp_mx_moe.py b/tests/kernels/moe/test_ocp_mx_moe.py
index 91b508d4163cc..5a850dda4f6fd 100644
--- a/tests/kernels/moe/test_ocp_mx_moe.py
+++ b/tests/kernels/moe/test_ocp_mx_moe.py
@@ -70,12 +70,12 @@ def test_mxfp4_loading_and_execution_moe(vllm_runner, model_case: ModelCase):
             f"{torch.cuda.device_count()}"
         )
 
-    # `cuda_graph_sizes=[16]` to reduce load time.
+    # `cudagraph_capture_sizes=[16]` to reduce load time.
     with vllm_runner(
         model_case.model_id,
         tensor_parallel_size=model_case.tp,
         load_format="dummy",
-        cuda_graph_sizes=[16],
+        cudagraph_capture_sizes=[16],
     ) as llm:
         # Disabled as check_model is broken: https://github.com/vllm-project/vllm/pull/18465#issuecomment-3329880562
         # def check_model(model):
diff --git a/tests/quantization/test_quark.py b/tests/quantization/test_quark.py
index 334f9a65e4c03..0ff6e8407ce67 100644
--- a/tests/quantization/test_quark.py
+++ b/tests/quantization/test_quark.py
@@ -212,11 +212,11 @@ def test_ocp_mx_wikitext_correctness(config: AccuracyTestConfig, tp_size: int):
     task = "wikitext"
     rtol = 0.1
 
-    # Smaller cuda_graph_sizes to speed up the test.
+    # Smaller cudagraph_capture_sizes to speed up the test.
     results = lm_eval.simple_evaluate(
         model="vllm",
         model_args=config.get_model_args(
-            tp_size=tp_size, kwargs={"cuda_graph_sizes": [16]}
+            tp_size=tp_size, kwargs={"cudagraph_capture_sizes": [16]}
         ),
         tasks=task,
         batch_size=64,
diff --git a/tests/test_config.py b/tests/test_config.py
index 77d3a7115978e..0768c6d2cddf5 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -1085,7 +1085,7 @@ def test_vllm_config_explicit_overrides():
     )
 
     # Override one field but not others
-    pass_config = PassConfig(enable_noop=False)
+    pass_config = PassConfig(eliminate_noops=False)
     compilation_config = CompilationConfig(pass_config=pass_config)
     config = VllmConfig(
         model_config=regular_model,
diff --git a/vllm/attention/backends/registry.py b/vllm/attention/backends/registry.py
index 125e4e3827747..eaa0fa1d5db39 100644
--- a/vllm/attention/backends/registry.py
+++ b/vllm/attention/backends/registry.py
@@ -252,35 +252,3 @@ def register_backend(
         return lambda x: x
 
     return decorator
-
-
-# Backwards compatibility alias for plugins
-class _BackendMeta(type):
-    """Metaclass to provide deprecation warnings when accessing _Backend."""
-
-    def __getattribute__(cls, name: str):
-        if name not in ("__class__", "__mro__", "__name__"):
-            logger.warning(
-                "_Backend has been renamed to AttentionBackendEnum. "
-                "Please update your code to use AttentionBackendEnum instead. "
-                "_Backend will be removed in a future release."
-            )
-        return getattr(AttentionBackendEnum, name)
-
-    def __getitem__(cls, name: str):
-        logger.warning(
-            "_Backend has been renamed to AttentionBackendEnum. "
-            "Please update your code to use AttentionBackendEnum instead. "
-            "_Backend will be removed in a future release."
-        )
-        return AttentionBackendEnum[name]
-
-
-class _Backend(metaclass=_BackendMeta):
-    """Deprecated: Use AttentionBackendEnum instead.
-
-    This class is provided for backwards compatibility with plugins
-    and will be removed in a future release.
-    """
-
-    pass
diff --git a/vllm/attention/selector.py b/vllm/attention/selector.py
index f6aba271d2e96..bbf95ff009001 100644
--- a/vllm/attention/selector.py
+++ b/vllm/attention/selector.py
@@ -1,7 +1,6 @@
 # SPDX-License-Identifier: Apache-2.0
 # SPDX-FileCopyrightText: Copyright contributors to the vLLM project
 
-import inspect
 from functools import cache
 from typing import cast, get_args
 
@@ -73,39 +72,18 @@ def _cached_get_attn_backend(
 ) -> type[AttentionBackend]:
     from vllm.platforms import current_platform
 
-    sig = inspect.signature(current_platform.get_attn_backend_cls)
-    if "use_v1" in sig.parameters:
-        logger.warning_once(
-            "use_v1 parameter for get_attn_backend_cls is deprecated and will "
-            "be removed in v0.13.0 or v1.0.0, whichever is soonest. Please "
-            "remove it from your plugin code."
-        )
-        attention_cls = current_platform.get_attn_backend_cls(
-            backend,
-            head_size,
-            dtype,
-            kv_cache_dtype,
-            block_size,
-            True,  # use_v1
-            use_mla,
-            has_sink,
-            use_sparse,
-            use_mm_prefix,
-            attn_type,
-        )
-    else:
-        attention_cls = current_platform.get_attn_backend_cls(
-            backend,
-            head_size,
-            dtype,
-            kv_cache_dtype,
-            block_size,
-            use_mla,
-            has_sink,
-            use_sparse,
-            use_mm_prefix,
-            attn_type,
-        )
+    attention_cls = current_platform.get_attn_backend_cls(
+        backend,
+        head_size,
+        dtype,
+        kv_cache_dtype,
+        block_size,
+        use_mla,
+        has_sink,
+        use_sparse,
+        use_mm_prefix,
+        attn_type,
+    )
     if not attention_cls:
         raise ValueError(
             f"Invalid attention backend for {current_platform.device_name}"
diff --git a/vllm/config/compilation.py b/vllm/config/compilation.py
index 51e4912aad9db..3b6cb8a343608 100644
--- a/vllm/config/compilation.py
+++ b/vllm/config/compilation.py
@@ -17,7 +17,6 @@ from vllm.config.utils import (
     Range,
     config,
     get_hash_factors,
-    handle_deprecated,
     hash_factors,
 )
 from vllm.logger import init_logger
@@ -127,27 +126,6 @@ class PassConfig:
     fuse_allreduce_rms: bool = Field(default=None)
     """Enable flashinfer allreduce fusion."""
 
-    # Deprecated flags
-    enable_fusion: bool = Field(default=None)
-    """Deprecated in: v0.12.0. Use fuse_norm_quant and fuse_act_quant 
-    instead. Will be removed in v0.13.0 or v1.0.0, whichever is sooner.
-    """
-    enable_attn_fusion: bool = Field(default=None)
-    """Deprecated in: v0.12.0. Use fuse_attn_quant instead. 
-    Will be removed in v0.13.0 or v1.0.0, whichever is sooner."""
-    enable_noop: bool = Field(default=None)
-    """Deprecated in: v0.12.0. Use eliminate_noops instead. 
-    Will be removed in v0.13.0 or v1.0.0, whichever is sooner."""
-    enable_sequence_parallelism: bool = Field(default=None)
-    """Deprecated in: v0.12.0. Use enable_sp instead. 
-    Will be removed in v0.13.0 or v1.0.0, whichever is sooner."""
-    enable_async_tp: bool = Field(default=None)
-    """Deprecated in: v0.12.0. Use fuse_gemm_comms instead. 
-    Will be removed in v0.13.0 or v1.0.0, whichever is sooner."""
-    enable_fi_allreduce_fusion: bool = Field(default=None)
-    """Deprecated in: v0.12.0. Use fuse_allreduce_rms instead. 
-    Will be removed in v0.13.0 or v1.0.0, whichever is sooner."""
-
     fi_allreduce_fusion_max_size_mb: float | None = None
     """The threshold of the communicated tensor sizes under which
     vllm should use flashinfer fused allreduce. Specified as a
@@ -206,15 +184,7 @@ class PassConfig:
         Any future fields that don't affect compilation should be excluded.
         """
 
-        ignored_fields = [
-            "enable_fusion",
-            "enable_attn_fusion",
-            "enable_noop",
-            "enable_sequence_parallelism",
-            "enable_async_tp",
-            "enable_fi_allreduce_fusion",
-        ]
-        return hash_factors(get_hash_factors(self, ignored_factors=ignored_fields))
+        return hash_factors(get_hash_factors(self, set()))
 
     @field_validator(
         "fuse_norm_quant",
@@ -224,12 +194,6 @@ class PassConfig:
         "enable_sp",
         "fuse_gemm_comms",
         "fuse_allreduce_rms",
-        "enable_fusion",
-        "enable_attn_fusion",
-        "enable_noop",
-        "enable_sequence_parallelism",
-        "enable_async_tp",
-        "enable_fi_allreduce_fusion",
         mode="wrap",
     )
     @classmethod
@@ -242,49 +206,6 @@ class PassConfig:
     def __post_init__(self) -> None:
         # Handle deprecation and defaults
 
-        # Map old flags to new flags and issue warnings
-        handle_deprecated(
-            self,
-            "enable_fusion",
-            ["fuse_norm_quant", "fuse_act_quant"],
-            "v0.13.0 or v1.0.0, whichever is sooner",
-        )
-
-        handle_deprecated(
-            self,
-            "enable_attn_fusion",
-            "fuse_attn_quant",
-            "v0.13.0 or v1.0.0, whichever is sooner",
-        )
-
-        handle_deprecated(
-            self,
-            "enable_sequence_parallelism",
-            "enable_sp",
-            "v0.13.0 or v1.0.0, whichever is sooner",
-        )
-
-        handle_deprecated(
-            self,
-            "enable_async_tp",
-            "fuse_gemm_comms",
-            "v0.13.0 or v1.0.0, whichever is sooner",
-        )
-
-        handle_deprecated(
-            self,
-            "enable_fi_allreduce_fusion",
-            "fuse_allreduce_rms",
-            "v0.13.0 or v1.0.0, whichever is sooner",
-        )
-
-        handle_deprecated(
-            self,
-            "enable_noop",
-            "eliminate_noops",
-            "v0.13.0 or v1.0.0, whichever is sooner",
-        )
-
         if not self.eliminate_noops:
             if self.fuse_norm_quant or self.fuse_act_quant:
                 logger.warning_once(
diff --git a/vllm/config/vllm.py b/vllm/config/vllm.py
index 607bb44cddd26..a3a9eec9b3203 100644
--- a/vllm/config/vllm.py
+++ b/vllm/config/vllm.py
@@ -1014,7 +1014,7 @@ class VllmConfig:
         max_graph_size = min(max_num_seqs * 2, 512)
         # 1, 2, 4, then multiples of 8 up to 256 and then multiples of 16
         # up to max_graph_size
-        cuda_graph_sizes = [1, 2, 4] + list(range(8, 256, 8)) + list(
+        cudagraph_capture_sizes = [1, 2, 4] + list(range(8, 256, 8)) + list(
             range(256, max_graph_size + 1, 16))
 
         In the end, `vllm_config.compilation_config.cudagraph_capture_sizes`
diff --git a/vllm/engine/arg_utils.py b/vllm/engine/arg_utils.py
index 2f307a7ccf16d..cbb4862434a98 100644
--- a/vllm/engine/arg_utils.py
+++ b/vllm/engine/arg_utils.py
@@ -375,7 +375,6 @@ class EngineArgs:
     kv_cache_dtype: CacheDType = CacheConfig.cache_dtype
     seed: int | None = 0
     max_model_len: int | None = ModelConfig.max_model_len
-    cuda_graph_sizes: list[int] | None = CompilationConfig.cudagraph_capture_sizes
     cudagraph_capture_sizes: list[int] | None = (
         CompilationConfig.cudagraph_capture_sizes
     )
@@ -1121,15 +1120,6 @@ class EngineArgs:
         compilation_group.add_argument(
             "--cudagraph-capture-sizes", **compilation_kwargs["cudagraph_capture_sizes"]
         )
-        compilation_kwargs["cudagraph_capture_sizes"]["help"] = (
-            "--cuda-graph-sizes is deprecated and will be removed in v0.13.0 or v1.0.0,"
-            " whichever is soonest. Please use --cudagraph-capture-sizes instead."
-        )
-        compilation_group.add_argument(
-            "--cuda-graph-sizes",
-            **compilation_kwargs["cudagraph_capture_sizes"],
-            deprecated=True,
-        )
         compilation_group.add_argument(
             "--max-cudagraph-capture-size",
             **compilation_kwargs["max_cudagraph_capture_size"],
@@ -1741,18 +1731,6 @@ class EngineArgs:
 
         # Compilation config overrides
         compilation_config = copy.deepcopy(self.compilation_config)
-        if self.cuda_graph_sizes is not None:
-            logger.warning(
-                "--cuda-graph-sizes is deprecated and will be removed in v0.13.0 or "
-                "v1.0.0, whichever is soonest. Please use --cudagraph-capture-sizes "
-                "instead."
-            )
-            if compilation_config.cudagraph_capture_sizes is not None:
-                raise ValueError(
-                    "cuda_graph_sizes and compilation_config."
-                    "cudagraph_capture_sizes are mutually exclusive"
-                )
-            compilation_config.cudagraph_capture_sizes = self.cuda_graph_sizes
         if self.cudagraph_capture_sizes is not None:
             if compilation_config.cudagraph_capture_sizes is not None:
                 raise ValueError(