diff --git a/script/determine-jobs.py b/script/determine-jobs.py
index 8039aff83f9..e4d002975c6 100755
--- a/script/determine-jobs.py
+++ b/script/determine-jobs.py
@@ -63,6 +63,7 @@ from helpers import (
     CPP_FILE_EXTENSIONS,
     ESPHOME_TESTS_COMPONENTS_PATH,
     PYTHON_FILE_EXTENSIONS,
+    base_python_changed,
     changed_files,
     core_changed,
     filter_component_and_test_cpp_files,
@@ -657,16 +658,20 @@ BENCHMARK_INFRASTRUCTURE_FILES = frozenset(
 
 
 def should_run_benchmarks(branch: str | None = None) -> bool:
-    """Determine if C++ benchmarks should run based on changed files.
+    """Determine if benchmarks (C++ and Python) should run based on changed files.
 
     Benchmarks run when any of the following conditions are met:
 
-    1. Core C++ files changed (esphome/core/*)
-    2. The host platform changed (esphome/components/host/*) — benchmarks
+    1. Core files changed (esphome/core/*, C++ or Python)
+    2. Top-level Python files changed (esphome/*.py and esphome/*.pyi) —
+       the Python benchmarks exercise config loading (config.py,
+       yaml_util.py, ...), so a slowdown there is invisible unless the
+       benchmarks job runs
+    3. The host platform changed (esphome/components/host/*) — benchmarks
        are built and run on the host platform, so its implementations of
        ``millis()``/``micros()``/etc. affect every benchmark
-    3. A directly changed component has benchmark files (no dependency expansion)
-    4. Benchmark infrastructure changed (tests/benchmarks/*, script/cpp_benchmark.py,
+    4. A directly changed component has benchmark files (no dependency expansion)
+    5. Benchmark infrastructure changed (tests/benchmarks/*, script/cpp_benchmark.py,
        script/build_helpers.py, script/setup_codspeed_lib.py)
 
     Unlike unit tests, benchmarks do NOT expand to dependent components.
@@ -683,6 +688,11 @@ def should_run_benchmarks(branch: str | None = None) -> bool:
     if core_changed(files):
         return True
 
+    # Top-level esphome/*.py modules are what the Python benchmarks in
+    # tests/benchmarks/python/ exercise
+    if base_python_changed(files):
+        return True
+
     # Host platform supplies the runtime that benchmarks execute on
     if any(f.startswith("esphome/components/host/") for f in files):
         return True
diff --git a/script/helpers.py b/script/helpers.py
index 6ba093b413a..7cc001d92f5 100644
--- a/script/helpers.py
+++ b/script/helpers.py
@@ -1380,6 +1380,27 @@ def core_changed(files: list[str]) -> bool:
     )
 
 
+def base_python_changed(files: list[str]) -> bool:
+    """Check if any Python file directly in esphome/ has changed.
+
+    Matches top-level modules and stubs (.py and .pyi) like esphome/config.py
+    and esphome/yaml_util.py but not files in subdirectories such as
+    esphome/components/ or esphome/dashboard/.
+
+    Args:
+        files: List of file paths to check
+
+    Returns:
+        True if any top-level esphome Python file has changed
+    """
+    return any(
+        f.startswith("esphome/")
+        and f.endswith(PYTHON_FILE_EXTENSIONS)
+        and "/" not in f.removeprefix("esphome/")
+        for f in files
+    )
+
+
 def get_cpp_changed_components(files: list[str]) -> list[str]:
     """Get components that have changed C++ files or tests.
 
diff --git a/tests/script/test_determine_jobs.py b/tests/script/test_determine_jobs.py
index a05b683a5ff..80f572d9fe6 100644
--- a/tests/script/test_determine_jobs.py
+++ b/tests/script/test_determine_jobs.py
@@ -2475,6 +2475,35 @@ def test_should_run_benchmarks_core_header_change() -> None:
         assert determine_jobs.should_run_benchmarks() is True
 
 
+def test_should_run_benchmarks_top_level_python_change() -> None:
+    """Test benchmarks trigger on top-level esphome Python module changes.
+
+    The Python benchmarks exercise config loading, so changes to modules
+    like config.py and yaml_util.py must run them; a regression in #16718
+    went unnoticed because these files matched no trigger.
+    """
+    for py_file in [
+        "esphome/config.py",
+        "esphome/yaml_util.py",
+        "esphome/__main__.py",
+        "esphome/helpers.py",
+    ]:
+        with patch.object(determine_jobs, "changed_files", return_value=[py_file]):
+            assert determine_jobs.should_run_benchmarks() is True, (
+                f"Expected benchmarks to run for {py_file}"
+            )
+
+
+def test_should_run_benchmarks_nested_python_change() -> None:
+    """Test benchmarks do NOT trigger for nested non-core Python changes."""
+    with patch.object(
+        determine_jobs,
+        "changed_files",
+        return_value=["esphome/dashboard/web_server.py"],
+    ):
+        assert determine_jobs.should_run_benchmarks() is False
+
+
 def test_should_run_benchmarks_host_platform_change() -> None:
     """Test benchmarks trigger on host platform changes.
 
diff --git a/tests/script/test_helpers.py b/tests/script/test_helpers.py
index 43c4445dcfc..077b6ef23e5 100644
--- a/tests/script/test_helpers.py
+++ b/tests/script/test_helpers.py
@@ -1851,3 +1851,24 @@ def test_get_component_test_files_component_without_tests(
 )
 def test_is_validate_only_file(filename: str, expected: bool, tmp_path: Path) -> None:
     assert helpers.is_validate_only_file(tmp_path / filename) is expected
+
+
+@pytest.mark.parametrize(
+    ("files", "expected"),
+    [
+        (["esphome/config.py"], True),
+        (["esphome/yaml_util.py"], True),
+        (["esphome/__main__.py"], True),
+        (["esphome/const.pyi"], True),
+        (["README.md", "esphome/helpers.py"], True),
+        (["esphome/core/config.py"], False),
+        (["esphome/components/sensor/__init__.py"], False),
+        (["esphome/dashboard/web_server.py"], False),
+        (["esphome/idf_component.yml"], False),
+        (["tests/unit_tests/test_config.py"], False),
+        ([], False),
+    ],
+)
+def test_base_python_changed(files: list[str], expected: bool) -> None:
+    """Only Python modules directly in esphome/ count as base Python changes."""
+    assert helpers.base_python_changed(files) is expected