diff --git a/src/cloudai/models/scenario.py b/src/cloudai/models/scenario.py
index 276cac2e5..751915095 100644
--- a/src/cloudai/models/scenario.py
+++ b/src/cloudai/models/scenario.py
@@ -1,5 +1,5 @@
 # SPDX-FileCopyrightText: NVIDIA CORPORATION & AFFILIATES
-# Copyright (c) 2024-2025 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+# Copyright (c) 2024-2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
 # SPDX-License-Identifier: Apache-2.0
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -108,7 +108,7 @@ def tdef_model_dump(self, by_alias: bool) -> dict:
             "extra_env_vars": self.extra_env_vars if self.extra_env_vars else None,
             "cmd_args": self.cmd_args.model_dump(by_alias=by_alias) if self.cmd_args else None,
             "git_repos": [repo.model_dump() for repo in self.git_repos] if self.git_repos else None,
-            "nsys": self.nsys.model_dump() if self.nsys else None,
+            "nsys": self.nsys.model_dump(exclude_unset=True) if self.nsys else None,
         }
         return {k: v for k, v in data.items() if v is not None}
 
diff --git a/tests/test_test_scenario.py b/tests/test_test_scenario.py
index c2af1373b..9e305d093 100644
--- a/tests/test_test_scenario.py
+++ b/tests/test_test_scenario.py
@@ -1,5 +1,5 @@
 # SPDX-FileCopyrightText: NVIDIA CORPORATION & AFFILIATES
-# Copyright (c) 2024-2025 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+# Copyright (c) 2024-2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
 # SPDX-License-Identifier: Apache-2.0
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -515,3 +515,160 @@ def test_get_reporters_nccl(self):
         assert len(reporters) == 2
         assert NcclTestPerformanceReportGenerationStrategy in reporters
         assert NcclTestPredictionReportGenerationStrategy in reporters
+
+
+class TestNsysMerging:
+    def test_nsys_partial_override_preserves_base_config(
+        self, test_scenario_parser: TestScenarioParser, slurm_system: SlurmSystem
+    ):
+        from cloudai.core import NsysConfiguration
+
+        test_scenario_parser.test_mapping = {
+            "nccl": NCCLTestDefinition(
+                name="nccl",
+                description="desc",
+                test_template_name="NcclTest",
+                cmd_args=NCCLCmdArgs(docker_image_url="fake://url/nccl"),
+                nsys=NsysConfiguration(
+                    enable=True,
+                    nsys_binary="/custom/nsys",
+                    output="/base/output",
+                    trace="cuda,nvtx",
+                    sample="cpu",
+                ),
+            )
+        }
+        model = TestScenarioModel.model_validate(
+            toml.loads(
+                """
+            name = "test"
+
+            [[Tests]]
+            id = "1"
+            test_name = "nccl"
+
+              [Tests.nsys]
+              output = "/scenario/output"
+            """
+            )
+        )
+        tdef = test_scenario_parser._prepare_tdef(model.tests[0])
+
+        assert tdef.nsys is not None
+        assert tdef.nsys.output == "/scenario/output"
+        assert tdef.nsys.nsys_binary == "/custom/nsys"
+        assert tdef.nsys.trace == "cuda,nvtx"
+        assert tdef.nsys.sample == "cpu"
+        assert tdef.nsys.enable is True
+
+    def test_nsys_multiple_fields_override(self, test_scenario_parser: TestScenarioParser, slurm_system: SlurmSystem):
+        from cloudai.core import NsysConfiguration
+
+        test_scenario_parser.test_mapping = {
+            "nccl": NCCLTestDefinition(
+                name="nccl",
+                description="desc",
+                test_template_name="NcclTest",
+                cmd_args=NCCLCmdArgs(docker_image_url="fake://url/nccl"),
+                nsys=NsysConfiguration(
+                    enable=True,
+                    nsys_binary="/base/nsys",
+                    output="/base/output",
+                    trace="cuda",
+                    force_overwrite=False,
+                ),
+            )
+        }
+        model = TestScenarioModel.model_validate(
+            toml.loads(
+                """
+            name = "test"
+
+            [[Tests]]
+            id = "1"
+            test_name = "nccl"
+
+              [Tests.nsys]
+              output = "/new/output"
+              force_overwrite = true
+            """
+            )
+        )
+        tdef = test_scenario_parser._prepare_tdef(model.tests[0])
+
+        assert tdef.nsys is not None
+        assert tdef.nsys.output == "/new/output"
+        assert tdef.nsys.force_overwrite is True
+        assert tdef.nsys.nsys_binary == "/base/nsys"
+        assert tdef.nsys.trace == "cuda"
+        assert tdef.nsys.enable is True
+
+    def test_nsys_scenario_adds_to_base_without_nsys(
+        self, test_scenario_parser: TestScenarioParser, slurm_system: SlurmSystem
+    ):
+        test_scenario_parser.test_mapping = {
+            "nccl": NCCLTestDefinition(
+                name="nccl",
+                description="desc",
+                test_template_name="NcclTest",
+                cmd_args=NCCLCmdArgs(docker_image_url="fake://url/nccl"),
+                # No nsys in base config
+            )
+        }
+        model = TestScenarioModel.model_validate(
+            toml.loads(
+                """
+            name = "test"
+
+            [[Tests]]
+            id = "1"
+            test_name = "nccl"
+
+              [Tests.nsys]
+              output = "/scenario/output"
+              trace = "cuda,nvtx"
+            """
+            )
+        )
+        tdef = test_scenario_parser._prepare_tdef(model.tests[0])
+
+        assert tdef.nsys is not None
+        assert tdef.nsys.output == "/scenario/output"
+        assert tdef.nsys.trace == "cuda,nvtx"
+        assert tdef.nsys.enable is True
+        assert tdef.nsys.nsys_binary == "nsys"
+
+    def test_nsys_disable_override(self, test_scenario_parser: TestScenarioParser, slurm_system: SlurmSystem):
+        from cloudai.core import NsysConfiguration
+
+        test_scenario_parser.test_mapping = {
+            "nccl": NCCLTestDefinition(
+                name="nccl",
+                description="desc",
+                test_template_name="NcclTest",
+                cmd_args=NCCLCmdArgs(docker_image_url="fake://url/nccl"),
+                nsys=NsysConfiguration(
+                    enable=True,
+                    output="/base/output",
+                ),
+            )
+        }
+        model = TestScenarioModel.model_validate(
+            toml.loads(
+                """
+            name = "test"
+
+            [[Tests]]
+            id = "1"
+            test_name = "nccl"
+
+              [Tests.nsys]
+              enable = false
+            """
+            )
+        )
+        tdef = test_scenario_parser._prepare_tdef(model.tests[0])
+
+        assert tdef.nsys is not None
+        assert tdef.nsys.enable is False
+        assert tdef.nsys.output == "/base/output"