diff --git a/doc/changes/devel/12986.bugfix.rst b/doc/changes/devel/12986.bugfix.rst
new file mode 100644
index 00000000000..5bacb548fdd
--- /dev/null
+++ b/doc/changes/devel/12986.bugfix.rst
@@ -0,0 +1 @@
+Fix IndexError when loading CNT file does not have annotations, by :newcontrib:`Ziyi ZENG`.
\ No newline at end of file
diff --git a/doc/changes/names.inc b/doc/changes/names.inc
index 79fbe9b1236..3dfc742b3b3 100644
--- a/doc/changes/names.inc
+++ b/doc/changes/names.inc
@@ -318,4 +318,5 @@
 .. _Yousra Bekhti: https://www.linkedin.com/pub/yousra-bekhti/56/886/421
 .. _Yu-Han Luo: https://github.com/yh-luo
 .. _Zhi Zhang: https://github.com/tczhangzhi/
+.. _Ziyi ZENG: https://github.com/ZiyiTsang
 .. _Zvi Baratz: https://github.com/ZviBaratz
diff --git a/mne/io/cnt/cnt.py b/mne/io/cnt/cnt.py
index bd5fb4c2f29..16c074269bf 100644
--- a/mne/io/cnt/cnt.py
+++ b/mne/io/cnt/cnt.py
@@ -337,7 +337,8 @@ def _get_cnt_info(input_fname, eog, ecg, emg, misc, data_format, date_format, he
                 n_samples = data_size // (n_bytes * n_channels)
                 # See: PR #12393
                 annotations = _read_annotations_cnt(input_fname, data_format="int16")
-                if annotations.onset[-1] * sfreq > n_samples:
+                # See: PR #12986
+                if len(annotations) and annotations.onset[-1] * sfreq > n_samples:
                     n_bytes = 4
                     n_samples = n_samples_header
                     warn(