diff --git a/builtin/fetch.c b/builtin/fetch.c
index f1570e3464..b5ad09d046 100644
--- a/builtin/fetch.c
+++ b/builtin/fetch.c
@@ -1177,7 +1177,7 @@ static int add_remote_or_group(const char *name, struct string_list *list)
 	git_config(get_remote_group, &g);
 	if (list->nr == prev_nr) {
 		struct remote *remote = remote_get(name);
-		if (!remote_is_configured(remote))
+		if (!remote_is_configured(remote, 0))
 			return 0;
 		string_list_append(list, remote->name);
 	}
diff --git a/builtin/remote.c b/builtin/remote.c
index e52cf3925b..5339ed6ad1 100644
--- a/builtin/remote.c
+++ b/builtin/remote.c
@@ -186,7 +186,7 @@ static int add(int argc, const char **argv)
 	url = argv[1];
 
 	remote = remote_get(name);
-	if (remote_is_configured(remote))
+	if (remote_is_configured(remote, 1))
 		die(_("remote %s already exists."), name);
 
 	strbuf_addf(&buf2, "refs/heads/test:refs/remotes/%s/test", name);
@@ -618,14 +618,14 @@ static int mv(int argc, const char **argv)
 	rename.remote_branches = &remote_branches;
 
 	oldremote = remote_get(rename.old);
-	if (!remote_is_configured(oldremote))
+	if (!remote_is_configured(oldremote, 1))
 		die(_("No such remote: %s"), rename.old);
 
 	if (!strcmp(rename.old, rename.new) && oldremote->origin != REMOTE_CONFIG)
 		return migrate_file(oldremote);
 
 	newremote = remote_get(rename.new);
-	if (remote_is_configured(newremote))
+	if (remote_is_configured(newremote, 1))
 		die(_("remote %s already exists."), rename.new);
 
 	strbuf_addf(&buf, "refs/heads/test:refs/remotes/%s/test", rename.new);
@@ -753,7 +753,7 @@ static int rm(int argc, const char **argv)
 		usage_with_options(builtin_remote_rm_usage, options);
 
 	remote = remote_get(argv[1]);
-	if (!remote_is_configured(remote))
+	if (!remote_is_configured(remote, 1))
 		die(_("No such remote: %s"), argv[1]);
 
 	known_remotes.to_delete = remote;
@@ -1415,7 +1415,7 @@ static int set_remote_branches(const char *remotename, const char **branches,
 	strbuf_addf(&key, "remote.%s.fetch", remotename);
 
 	remote = remote_get(remotename);
-	if (!remote_is_configured(remote))
+	if (!remote_is_configured(remote, 1))
 		die(_("No such remote '%s'"), remotename);
 
 	if (!add_mode && remove_all_fetch_refspecs(remotename, key.buf)) {
@@ -1469,7 +1469,7 @@ static int get_url(int argc, const char **argv)
 	remotename = argv[0];
 
 	remote = remote_get(remotename);
-	if (!remote_is_configured(remote))
+	if (!remote_is_configured(remote, 1))
 		die(_("No such remote '%s'"), remotename);
 
 	url_nr = 0;
@@ -1537,7 +1537,7 @@ static int set_url(int argc, const char **argv)
 		oldurl = newurl;
 
 	remote = remote_get(remotename);
-	if (!remote_is_configured(remote))
+	if (!remote_is_configured(remote, 1))
 		die(_("No such remote '%s'"), remotename);
 
 	if (push_mode) {
diff --git a/remote.c b/remote.c
index d5eaec7374..bf1bf23091 100644
--- a/remote.c
+++ b/remote.c
@@ -255,6 +255,7 @@ static void read_remotes_file(struct remote *remote)
 
 	if (!f)
 		return;
+	remote->configured_in_repo = 1;
 	remote->origin = REMOTE_REMOTES;
 	while (strbuf_getline(&buf, f) != EOF) {
 		const char *v;
@@ -289,6 +290,7 @@ static void read_branches_file(struct remote *remote)
 		return;
 	}
 
+	remote->configured_in_repo = 1;
 	remote->origin = REMOTE_BRANCHES;
 
 	/*
@@ -371,6 +373,8 @@ static int handle_config(const char *key, const char *value, void *cb)
 	}
 	remote = make_remote(name, namelen);
 	remote->origin = REMOTE_CONFIG;
+	if (current_config_scope() == CONFIG_SCOPE_REPO)
+		remote->configured_in_repo = 1;
 	if (!strcmp(subkey, "mirror"))
 		remote->mirror = git_config_bool(key, value);
 	else if (!strcmp(subkey, "skipdefaultupdate"))
@@ -714,9 +718,13 @@ struct remote *pushremote_get(const char *name)
 	return remote_get_1(name, pushremote_for_branch);
 }
 
-int remote_is_configured(struct remote *remote)
+int remote_is_configured(struct remote *remote, int in_repo)
 {
-	return remote && remote->origin;
+	if (!remote)
+		return 0;
+	if (in_repo)
+		return remote->configured_in_repo;
+	return !!remote->origin;
 }
 
 int for_each_remote(each_remote_fn fn, void *priv)
diff --git a/remote.h b/remote.h
index 924881169d..a5bbbe0ef9 100644
--- a/remote.h
+++ b/remote.h
@@ -15,7 +15,7 @@ struct remote {
 	struct hashmap_entry ent;  /* must be first */
 
 	const char *name;
-	int origin;
+	int origin, configured_in_repo;
 
 	const char *foreign_vcs;
 
@@ -60,7 +60,7 @@ struct remote {
 
 struct remote *remote_get(const char *name);
 struct remote *pushremote_get(const char *name);
-int remote_is_configured(struct remote *remote);
+int remote_is_configured(struct remote *remote, int in_repo);
 
 typedef int each_remote_fn(struct remote *remote, void *priv);
 int for_each_remote(each_remote_fn fn, void *priv);
diff --git a/t/t5505-remote.sh b/t/t5505-remote.sh
index 8198d8eb05..ba46e86de0 100755
--- a/t/t5505-remote.sh
+++ b/t/t5505-remote.sh
@@ -764,6 +764,13 @@ test_expect_success 'rename a remote with name prefix of other remote' '
 	)
 '
 
+test_expect_success 'rename succeeds with existing remote.<target>.prune' '
+	git clone one four.four &&
+	test_when_finished git config --global --unset remote.upstream.prune &&
+	git config --global remote.upstream.prune true &&
+	git -C four.four remote rename origin upstream
+'
+
 cat >remotes_origin <<EOF
 URL: $(pwd)/one
 Push: refs/heads/master:refs/heads/upstream