diff --git a/compat/mingw.c b/compat/mingw.c
index 64e0c86579a5f0..72dcbd733cab1a 100644
--- a/compat/mingw.c
+++ b/compat/mingw.c
@@ -555,10 +555,25 @@ static int is_dir_empty(const wchar_t *wpath)
 int mingw_rmdir(const char *pathname)
 {
 	int tries = 0;
+	struct stat sb;
+
 	wchar_t wpathname[MAX_LONG_PATH];
 	if (xutftowcs_long_path(wpathname, pathname) < 0)
 		return -1;
 
+	/*
+	* Contrary to Linux rmdir(), Windows' _wrmdir() and _rmdir()
+	* will remove the directory at the path if it is a symbolic link
+	* which leads to issues when symlinks are used in the .git folder
+	* (in the context of git-repo for instance). So before calling _wrmdir()
+	* we first check if the path is a symbolic link. If it is, we exit
+	* and return the same error as Linux rmdir() in this case (ENOTDIR).
+	*/
+	if (!mingw_lstat(pathname, &sb) && S_ISLNK(sb.st_mode)) {
+		errno = ENOTDIR;
+		return -1;
+	}
+
 	do {
 		if (!_wrmdir(wpathname)) {
 			invalidate_lstat_cache();
diff --git a/t/t3400-rebase.sh b/t/t3400-rebase.sh
index 0bb88aa982beea..23dbd3c82ed6a2 100755
--- a/t/t3400-rebase.sh
+++ b/t/t3400-rebase.sh
@@ -406,4 +406,14 @@ test_expect_success 'refuse to switch to branch checked out elsewhere' '
 	test_i18ngrep "already checked out" err
 '
 
+test_expect_success MINGW,SYMLINKS_WINDOWS 'rebase when .git/logs is a symlink' '
+	git checkout main &&
+	mv .git/logs actual_logs &&
+	cmd //c "mklink /D .git\logs ..\actual_logs" &&
+	git rebase -f HEAD^ &&
+	test -L .git/logs &&
+	rm .git/logs &&
+	mv actual_logs .git/logs
+'
+
 test_done
diff --git a/t/test-lib.sh b/t/test-lib.sh
index 916d0a6b62fc13..d7e2315b4b9b61 100644
--- a/t/test-lib.sh
+++ b/t/test-lib.sh
@@ -1568,6 +1568,12 @@ test_lazy_prereq SYMLINKS '
 	ln -s x y && test -h y
 '
 
+test_lazy_prereq SYMLINKS_WINDOWS '
+	# test whether symbolic links are enabled on Windows
+	test_have_prereq MINGW &&
+	cmd //c "mklink y x" &> /dev/null && test -h y
+'
+
 test_lazy_prereq FILEMODE '
 	test "$(git config --bool core.filemode)" = true
 '