diff --git a/pre_commit/git.py b/pre_commit/git.py
index ec1928f37..1161be575 100644
--- a/pre_commit/git.py
+++ b/pre_commit/git.py
@@ -152,7 +152,8 @@ def intent_to_add_files() -> list[str]:
 
 
 def get_all_files() -> list[str]:
-    return zsplit(cmd_output('git', 'ls-files', '-z')[1])
+    # git ls-files lists unmerged paths once per stage -- deduplicate (#3706)
+    return list(dict.fromkeys(zsplit(cmd_output('git', 'ls-files', '-z')[1])))
 
 
 def get_changed_files(old: str, new: str) -> list[str]:
diff --git a/tests/git_test.py b/tests/git_test.py
index 02b6ce3ae..6658c4e4f 100644
--- a/tests/git_test.py
+++ b/tests/git_test.py
@@ -225,6 +225,14 @@ def test_all_files_non_ascii(non_ascii_repo):
     assert ret == ['интервью']
 
 
+def test_all_files_deduplicates_in_merge_conflict(in_merge_conflict):
+    # git ls-files lists each unmerged path once per stage; #3706
+    ret = git.get_all_files()
+    # The fixture contains multiple tracked files; the bug is duplication
+    assert ret.count('conflict_file') == 1
+    assert len(ret) == len(set(ret))
+
+
 def test_staged_files_non_ascii(non_ascii_repo):
     non_ascii_repo.join('интервью').write('hi')
     cmd_output('git', 'add', '.')