diff --git a/aeon/transformations/collection/_impute.py b/aeon/transformations/collection/_impute.py
index a145317820..26792b6dc8 100644
--- a/aeon/transformations/collection/_impute.py
+++ b/aeon/transformations/collection/_impute.py
@@ -118,7 +118,10 @@ def _transform(
                         x,
                     )
                 else:  # if strategy is a callable function
-                    x = np.where(np.isnan(x), self.strategy(x), x)
+                    n_channels = x.shape[0]
+                    for i in range(n_channels):
+                        nan_mask = np.isnan(x[i])
+                        x[i] = np.where(nan_mask, self.strategy(x[i][nan_mask]), x[i])
                 Xt.append(x)
 
             return Xt
diff --git a/aeon/transformations/collection/tests/test_simple_imputer.py b/aeon/transformations/collection/tests/test_simple_imputer.py
index d1bb168969..f1e4fb62a2 100644
--- a/aeon/transformations/collection/tests/test_simple_imputer.py
+++ b/aeon/transformations/collection/tests/test_simple_imputer.py
@@ -116,3 +116,23 @@ def test_valid_parameters():
 
     with pytest.raises(ValueError):
         imputer.fit_transform(X)
+
+
+def test_callable():
+    """Test SimpleImputer with callable strategy."""
+    X, _ = make_example_3d_numpy(
+        n_cases=10, n_channels=2, n_timepoints=50, random_state=42
+    )
+    X[2, 1, 10] = np.nan
+    X[5, 0, 20] = np.nan
+
+    def dummy_strategy(x):
+        return 0
+
+    imputer = SimpleImputer(strategy=dummy_strategy)
+    Xt = imputer.fit_transform(X)
+
+    assert not np.isnan(Xt).any()
+    assert Xt.shape == X.shape
+    assert np.allclose(Xt[2, 1, 10], 0)
+    assert np.allclose(Xt[5, 0, 20], 0)