diff --git a/package/CHANGELOG b/package/CHANGELOG
index 45647f3904..524f3918cb 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -23,6 +23,8 @@ The rules for this file:
  * 2.11.0
 
 Fixes
+ * `AnalysisBase.run()` now interprets NumPy boolean arrays passed to `frames`
+   as frame masks instead of integer frame indices (Issue #5472)
  * Mass (u) has been added to MDAnalysis base units and clarified that physical
    constants use CODATA 2010 values (Issue #3944, PR #5439)
  * Added `.gitattributes` to enforce LF (\n) as line endings and renormalized
diff --git a/package/MDAnalysis/analysis/base.py b/package/MDAnalysis/analysis/base.py
index f18b866951..8ab19be6db 100644
--- a/package/MDAnalysis/analysis/base.py
+++ b/package/MDAnalysis/analysis/base.py
@@ -616,7 +616,7 @@ def _setup_computation_groups(
         else:
             used_frames = frames
 
-        if all(isinstance(obj, bool) for obj in used_frames):
+        if all(isinstance(obj, (bool, np.bool_)) for obj in used_frames):
             arange = np.arange(len(used_frames))
             used_frames = arange[used_frames]
 
@@ -781,8 +781,10 @@ def run(
         step : int, optional
             number of frames to skip between each analysed frame
         frames : array_like, optional
-            array of integers or booleans to slice trajectory; ``frames`` can
-            only be used *instead* of ``start``, ``stop``, and ``step``. Setting
+            array of integers or booleans to slice trajectory. Boolean arrays,
+            including NumPy arrays, can be used as masks for fancy indexing.
+            ``frames`` can only be used *instead* of ``start``, ``stop``, and
+            ``step``. Setting
             *both* ``frames`` and at least one of ``start``, ``stop``, ``step``
             to a non-default value will raise a :exc:`ValueError`.
 
@@ -831,6 +833,10 @@ def run(
             Introduced ``backend``, ``n_workers``, ``n_parts`` and
             ``unsupported_backend`` keywords, and refactored the method logic to
             support parallelizable execution.
+
+        .. versionchanged:: 2.11.0
+            NumPy boolean arrays passed to ``frames`` are now interpreted as
+            boolean masks.
         """
         # default to serial execution
         backend = "serial" if backend is None else backend
diff --git a/testsuite/MDAnalysisTests/analysis/test_base.py b/testsuite/MDAnalysisTests/analysis/test_base.py
index 0dd872bde5..7fea26f1d5 100644
--- a/testsuite/MDAnalysisTests/analysis/test_base.py
+++ b/testsuite/MDAnalysisTests/analysis/test_base.py
@@ -337,6 +337,27 @@ def test_start_stop_step(u, run_kwargs, frames):
             },
             (0, 1, 3, 5, 6, 8),
         ),
+        pytest.param(
+            {
+                "frames": np.array(
+                    [
+                        True,
+                        True,
+                        False,
+                        True,
+                        False,
+                        True,
+                        True,
+                        False,
+                        True,
+                        False,
+                    ],
+                    dtype=bool,
+                )
+            },
+            (0, 1, 3, 5, 6, 8),
+            id="numpy-bool-mask",
+        ),
     ],
 )
 def test_frame_slice(u_xtc, run_kwargs, frames):
@@ -370,6 +391,27 @@ def test_frame_slice(u_xtc, run_kwargs, frames):
             },
             (0, 1, 3, 5, 6, 8),
         ),
+        pytest.param(
+            {
+                "frames": np.array(
+                    [
+                        True,
+                        True,
+                        False,
+                        True,
+                        False,
+                        True,
+                        True,
+                        False,
+                        True,
+                        False,
+                    ],
+                    dtype=bool,
+                )
+            },
+            (0, 1, 3, 5, 6, 8),
+            id="numpy-bool-mask",
+        ),
     ],
 )
 def test_frame_slice_parallel(run_kwargs, frames, client_FrameAnalysis):