diff --git a/doc/changes/dev/13894.bugfix.rst b/doc/changes/dev/13894.bugfix.rst
new file mode 100644
index 00000000000..c6af5316f06
--- /dev/null
+++ b/doc/changes/dev/13894.bugfix.rst
@@ -0,0 +1 @@
+Fix bug where ``picks`` was ignored in :meth:`mne.Epochs.apply_function` when ``channel_wise=False``, by `Thomas Binns`_.
\ No newline at end of file
diff --git a/mne/epochs.py b/mne/epochs.py
index 03fff949572..8aaf1316305 100644
--- a/mne/epochs.py
+++ b/mne/epochs.py
@@ -2045,7 +2045,7 @@ def apply_function(
                 for run_idx, ch_idx in enumerate(picks):
                     self._data[:, ch_idx, :] = data_picks_new[run_idx]
         else:
-            self._data = _check_fun(fun, data_in, **kwargs)
+            self._data[:, picks, :] = _check_fun(fun, data_in[:, picks, :], **kwargs)
 
         return self
 
diff --git a/mne/tests/test_epochs.py b/mne/tests/test_epochs.py
index 91c5f902ac8..1a66dc03eec 100644
--- a/mne/tests/test_epochs.py
+++ b/mne/tests/test_epochs.py
@@ -4832,20 +4832,21 @@ def test_apply_function():
     info = mne.create_info(n_channels, 1000.0, "eeg")
     epochs = mne.EpochsArray(data, info, events)
     data_epochs = epochs.get_data()
+    picks = np.arange(3)
+    non_picks = np.arange(3, n_channels)
 
     # apply_function to all channels at once
     def fun(data):
         """Reverse channel order without changing values."""
         return np.eye(data.shape[1])[::-1] @ data
 
-    want = data_epochs[:, ::-1]
-    got = epochs.apply_function(fun, channel_wise=False).get_data()
+    want = np.concatenate(
+        [data_epochs[:, picks][:, ::-1], data_epochs[:, non_picks]], axis=1
+    )  # only reverse channel order of picks
+    got = epochs.apply_function(fun, picks=picks, channel_wise=False).get_data()
     assert_array_equal(want, got)
 
     # apply_function channel-wise (to first 3 channels) by replacing with mean
-    picks = np.arange(3)
-    non_picks = np.arange(3, n_channels)
-
     def fun(data):
         return np.full_like(data, data.mean())