diff --git a/mne/io/edf/edf.py b/mne/io/edf/edf.py
index 7a82db8eecc..51e37a7a670 100644
--- a/mne/io/edf/edf.py
+++ b/mne/io/edf/edf.py
@@ -681,8 +681,9 @@ def _get_info(
         info["subject_info"]["weight"] = float(edf_info["subject_info"]["weight"])
 
     # Filter settings
-    _set_prefilter(info, edf_info, "highpass")
-    _set_prefilter(info, edf_info, "lowpass")
+    if filt_ch_idxs := [x for x in sel if x not in stim_channel_idxs]:
+        _set_prefilter(info, edf_info, filt_ch_idxs, "highpass")
+        _set_prefilter(info, edf_info, filt_ch_idxs, "lowpass")
 
     if np.isnan(info["lowpass"]):
         info["lowpass"] = info["sfreq"] / 2.0
@@ -746,9 +747,10 @@ def _prefilter_float(filt):
     return np.nan
 
 
-def _set_prefilter(info, edf_info, key):
+def _set_prefilter(info, edf_info, ch_idxs, key):
     value = 0
     if len(values := edf_info.get(key, [])):
+        values = [x for i, x in enumerate(values) if i in ch_idxs]
         if len(np.unique(values)) > 1:
             warn(
                 f"Channels contain different {key} filters. "
@@ -936,9 +938,7 @@ def _read_edf_header(fname, exclude, infer_types, include=None):
         digital_max = np.array([float(_edf_str_num(fid.read(8))) for ch in channels])[
             sel
         ]
-        prefiltering = np.array([_edf_str(fid.read(80)).strip() for ch in channels])[
-            sel
-        ]
+        prefiltering = np.array([_edf_str(fid.read(80)).strip() for ch in channels])
         highpass, lowpass = _parse_prefilter_string(prefiltering)
 
         # number of samples per record
diff --git a/mne/io/edf/tests/test_edf.py b/mne/io/edf/tests/test_edf.py
index 433b328d7a8..f8b327f4df8 100644
--- a/mne/io/edf/tests/test_edf.py
+++ b/mne/io/edf/tests/test_edf.py
@@ -710,7 +710,9 @@ def test_edf_set_prefilter(edf_info, hp, lp, hp_warn, lp_warn):
     else:
         ctx = nullcontext()
     with ctx:
-        _set_prefilter(info, edf_info, "highpass")
+        _set_prefilter(
+            info, edf_info, list(range(len(edf_info["highpass"]))), "highpass"
+        )
 
     if lp_warn:
         ctx = pytest.warns(
@@ -723,7 +725,7 @@ def test_edf_set_prefilter(edf_info, hp, lp, hp_warn, lp_warn):
     else:
         ctx = nullcontext()
     with ctx:
-        _set_prefilter(info, edf_info, "lowpass")
+        _set_prefilter(info, edf_info, list(range(len(edf_info["lowpass"]))), "lowpass")
     assert info["highpass"] == hp
     assert info["lowpass"] == lp
 
diff --git a/mne/report/tests/test_report.py b/mne/report/tests/test_report.py
index e8c4d018460..65d3ceb697a 100644
--- a/mne/report/tests/test_report.py
+++ b/mne/report/tests/test_report.py
@@ -310,13 +310,12 @@ def test_render_non_fiff(tmp_path):
         fnames_out.append(fname_out)
 
     report = Report()
-    with pytest.warns(RuntimeWarning, match="Channels contain different"):
-        report.parse_folder(
-            data_path=tmp_path,
-            render_bem=False,
-            on_error="raise",
-            raw_butterfly=False,
-        )
+    report.parse_folder(
+        data_path=tmp_path,
+        render_bem=False,
+        on_error="raise",
+        raw_butterfly=False,
+    )
 
     # Check correct paths and filenames
     _, _, content_titles, _ = report._content_as_html()