diff --git a/builtin/worktree.c b/builtin/worktree.c
index 02a5844705..9fe9e442c7 100644
--- a/builtin/worktree.c
+++ b/builtin/worktree.c
@@ -156,6 +156,16 @@ static int prune_cmp(const void *a, const void *b)
 
 	if ((c = fspathcmp(x->string, y->string)))
 	    return c;
+	/*
+	 * paths same; prune_dupes() removes all but the first worktree entry
+	 * having the same path, so sort main worktree ('util' is NULL) above
+	 * linked worktrees ('util' not NULL) since main worktree can't be
+	 * removed
+	 */
+	if (!x->util)
+		return -1;
+	if (!y->util)
+		return 1;
 	/* paths same; sort by .git/worktrees/<id> */
 	return strcmp(x->util, y->util);
 }
@@ -174,6 +184,7 @@ static void prune_dups(struct string_list *l)
 static void prune_worktrees(void)
 {
 	struct strbuf reason = STRBUF_INIT;
+	struct strbuf main_path = STRBUF_INIT;
 	struct string_list kept = STRING_LIST_INIT_NODUP;
 	DIR *dir = opendir(git_path("worktrees"));
 	struct dirent *d;
@@ -191,6 +202,10 @@ static void prune_worktrees(void)
 	}
 	closedir(dir);
 
+	strbuf_add_absolute_path(&main_path, get_git_common_dir());
+	/* massage main worktree absolute path to match 'gitdir' content */
+	strbuf_strip_suffix(&main_path, "/.");
+	string_list_append(&kept, strbuf_detach(&main_path, NULL));
 	prune_dups(&kept);
 	string_list_clear(&kept, 1);
 
diff --git a/t/t2401-worktree-prune.sh b/t/t2401-worktree-prune.sh
index fd3916fee0..a6ce7f590b 100755
--- a/t/t2401-worktree-prune.sh
+++ b/t/t2401-worktree-prune.sh
@@ -104,4 +104,16 @@ test_expect_success 'prune duplicate (linked/linked)' '
 	! test -d .git/worktrees/w2
 '
 
+test_expect_success 'prune duplicate (main/linked)' '
+	test_when_finished rm -fr repo wt &&
+	test_create_repo repo &&
+	test_commit -C repo x &&
+	git -C repo worktree add --detach ../wt &&
+	rm -fr wt &&
+	mv repo wt &&
+	git -C wt worktree prune --verbose >actual &&
+	test_i18ngrep "duplicate entry" actual &&
+	! test -d .git/worktrees/wt
+'
+
 test_done