diff --git a/src/wp-admin/includes/file.php b/src/wp-admin/includes/file.php
index 0c6d968ea02d3..8c9472300133a 100644
--- a/src/wp-admin/includes/file.php
+++ b/src/wp-admin/includes/file.php
@@ -149,10 +149,10 @@ function list_files( $folder = '', $levels = 100, $exclusions = array(), $includ
 
 	$files = array();
 
-	$dir = @opendir( $folder );
+	$results = @scandir( $folder );
 
-	if ( $dir ) {
-		while ( ( $file = readdir( $dir ) ) !== false ) {
+	if ( $results ) {
+		foreach ( $results as $file ) {
 			// Skip current and parent folder links.
 			if ( in_array( $file, array( '.', '..' ), true ) ) {
 				continue;
@@ -174,8 +174,6 @@ function list_files( $folder = '', $levels = 100, $exclusions = array(), $includ
 				$files[] = $folder . $file;
 			}
 		}
-
-		closedir( $dir );
 	}
 
 	return $files;
diff --git a/src/wp-admin/includes/misc.php b/src/wp-admin/includes/misc.php
index 3724684ffd428..d14ae1ab3d43b 100644
--- a/src/wp-admin/includes/misc.php
+++ b/src/wp-admin/includes/misc.php
@@ -355,6 +355,41 @@ function update_recently_edited( $file ) {
 	update_option( 'recently_edited', $oldfiles );
 }
 
+/**
+ * Sorts a file tree array with folders before files, both in alphabetical order.
+ *
+ * @since x.x.x
+ * @access private
+ *
+ * @param array $tree File tree to sort, as returned by wp_make_theme_file_tree()
+ *                    or wp_make_plugin_file_tree(). Directory nodes are arrays,
+ *                    file nodes are strings.
+ * @return array Sorted file tree.
+ */
+function _wp_sort_file_tree( $tree ) {
+	uksort(
+		$tree,
+		function ( $a, $b ) use ( $tree ) {
+			$a_is_dir = is_array( $tree[ $a ] );
+			$b_is_dir = is_array( $tree[ $b ] );
+
+			if ( $a_is_dir !== $b_is_dir ) {
+				return $a_is_dir ? -1 : 1;
+			}
+
+			return strcasecmp( $a, $b );
+		}
+	);
+
+	foreach ( $tree as $key => $subtree ) {
+		if ( is_array( $subtree ) ) {
+			$tree[ $key ] = _wp_sort_file_tree( $subtree );
+		}
+	}
+
+	return $tree;
+}
+
 /**
  * Makes a tree structure for the theme file editor's file list.
  *
@@ -378,6 +413,17 @@ function wp_make_theme_file_tree( $allowed_files ) {
 		$last_dir = $file_name;
 	}
 
+	$tree_list = _wp_sort_file_tree( $tree_list );
+
+	// Move the main theme files to the top of the list, preserving the order
+	// established by theme-editor.php (style.css first, then functions.php).
+	if ( isset( $tree_list['functions.php'] ) ) {
+		$tree_list = array( 'functions.php' => $tree_list['functions.php'] ) + $tree_list;
+	}
+	if ( isset( $tree_list['style.css'] ) ) {
+		$tree_list = array( 'style.css' => $tree_list['style.css'] ) + $tree_list;
+	}
+
 	return $tree_list;
 }
 
@@ -483,6 +529,16 @@ function wp_make_plugin_file_tree( $plugin_editable_files ) {
 		$last_dir = $plugin_file;
 	}
 
+	$tree_list = _wp_sort_file_tree( $tree_list );
+
+	// Move the main plugin file to the top of the list.
+	if ( ! empty( $plugin_editable_files ) ) {
+		$main_file_key = wp_basename( $plugin_editable_files[0] );
+		if ( isset( $tree_list[ $main_file_key ] ) ) {
+			$tree_list = array( $main_file_key => $tree_list[ $main_file_key ] ) + $tree_list;
+		}
+	}
+
 	return $tree_list;
 }
 
diff --git a/tests/phpunit/tests/admin/includesMisc.php b/tests/phpunit/tests/admin/includesMisc.php
index 2903ea1ca6e78..ccf69850aa3d4 100644
--- a/tests/phpunit/tests/admin/includesMisc.php
+++ b/tests/phpunit/tests/admin/includesMisc.php
@@ -28,6 +28,118 @@ public function test_shorten_url() {
 		}
 	}
 
+	/**
+	 * Tests that _wp_sort_file_tree() places folders before files, both alphabetically.
+	 *
+	 * @ticket 47544
+	 *
+	 * @covers ::_wp_sort_file_tree
+	 */
+	public function test_wp_sort_file_tree_folders_before_files() {
+		$tree = array(
+			'readme.txt'    => 'plugin/readme.txt',
+			'assets'        => array(
+				'logo.png' => 'plugin/assets/logo.png',
+			),
+			'composer.json' => 'plugin/composer.json',
+			'classes'       => array(
+				'Foo.php' => 'plugin/classes/Foo.php',
+			),
+		);
+
+		$sorted = _wp_sort_file_tree( $tree );
+		$keys   = array_keys( $sorted );
+
+		$this->assertSame( 0, array_search( 'assets', $keys, true ), 'assets folder should be first.' );
+		$this->assertSame( 1, array_search( 'classes', $keys, true ), 'classes folder should be second.' );
+		$this->assertSame( 2, array_search( 'composer.json', $keys, true ), 'composer.json file should be third.' );
+		$this->assertSame( 3, array_search( 'readme.txt', $keys, true ), 'readme.txt file should be last.' );
+	}
+
+	/**
+	 * Tests that _wp_sort_file_tree() sorts recursively within subdirectories.
+	 *
+	 * @ticket 47544
+	 *
+	 * @covers ::_wp_sort_file_tree
+	 */
+	public function test_wp_sort_file_tree_sorts_recursively() {
+		$tree = array(
+			'src' => array(
+				'zebra.php' => 'plugin/src/zebra.php',
+				'inc'       => array(
+					'b.php' => 'plugin/src/inc/b.php',
+					'a.php' => 'plugin/src/inc/a.php',
+				),
+				'apple.php' => 'plugin/src/apple.php',
+			),
+		);
+
+		$sorted   = _wp_sort_file_tree( $tree );
+		$src_keys = array_keys( $sorted['src'] );
+
+		$this->assertSame( 'inc', $src_keys[0], 'inc folder should be first inside src/.' );
+		$this->assertSame( 'apple.php', $src_keys[1], 'apple.php should be before zebra.php.' );
+		$this->assertSame( 'zebra.php', $src_keys[2], 'zebra.php should be last inside src/.' );
+
+		$inc_keys = array_keys( $sorted['src']['inc'] );
+		$this->assertSame( array( 'a.php', 'b.php' ), $inc_keys );
+	}
+
+	/**
+	 * Tests that wp_make_plugin_file_tree() places the main plugin file first,
+	 * then folders, then files, all alphabetically.
+	 *
+	 * @ticket 47544
+	 *
+	 * @covers ::wp_make_plugin_file_tree
+	 */
+	public function test_wp_make_plugin_file_tree_main_file_first_then_folders_then_files() {
+		$plugin_files = array(
+			'my-plugin/my-plugin.php',
+			'my-plugin/readme.txt',
+			'my-plugin/assets/logo.png',
+			'my-plugin/classes/Foo.php',
+			'my-plugin/composer.json',
+		);
+
+		$tree = wp_make_plugin_file_tree( $plugin_files );
+		$keys = array_keys( $tree );
+
+		$this->assertSame( 'my-plugin.php', $keys[0], 'Main plugin file should be first.' );
+		$this->assertSame( 'assets', $keys[1], 'assets folder should come before files.' );
+		$this->assertSame( 'classes', $keys[2], 'classes folder should come before files.' );
+		$this->assertSame( 'composer.json', $keys[3], 'composer.json should be sorted alphabetically among files.' );
+		$this->assertSame( 'readme.txt', $keys[4], 'readme.txt should be last.' );
+	}
+
+	/**
+	 * Tests that wp_make_theme_file_tree() places style.css first, functions.php
+	 * second, then folders, then files alphabetically.
+	 *
+	 * @ticket 47544
+	 *
+	 * @covers ::wp_make_theme_file_tree
+	 */
+	public function test_wp_make_theme_file_tree_main_files_first_then_folders_then_files() {
+		$allowed_files = array(
+			'readme.txt'     => '/theme/readme.txt',
+			'inc/extras.php' => '/theme/inc/extras.php',
+			'functions.php'  => '/theme/functions.php',
+			'style.css'      => '/theme/style.css',
+			'404.php'        => '/theme/404.php',
+		);
+
+		$tree = wp_make_theme_file_tree( $allowed_files );
+		$keys = array_keys( $tree );
+
+		$this->assertSame( 'style.css', $keys[0], 'style.css should be first.' );
+		$this->assertSame( 'functions.php', $keys[1], 'functions.php should be second.' );
+		$this->assertSame( 'inc', $keys[2], 'inc folder should come before loose files.' );
+		$this->assertSame( '404.php', $keys[3], '404.php should be sorted alphabetically among files.' );
+		$this->assertSame( 'readme.txt', $keys[4], 'readme.txt should be last.' );
+	}
+
 	/**
 	 * @ticket 59520
 	 */
diff --git a/tests/phpunit/tests/functions/listFiles.php b/tests/phpunit/tests/functions/listFiles.php
index a7e7346956dc6..25b9b4b30b0db 100644
--- a/tests/phpunit/tests/functions/listFiles.php
+++ b/tests/phpunit/tests/functions/listFiles.php
@@ -52,6 +52,32 @@ public function test_list_files_should_optionally_include_hidden_files( $filenam
 		}
 	}
 
+	/**
+	 * Tests that list_files() returns files in alphabetical order.
+	 *
+	 * @ticket 47544
+	 */
+	public function test_list_files_returns_files_in_alphabetical_order() {
+		$test_dir = get_temp_dir() . 'test-list-files-order/';
+		mkdir( $test_dir );
+
+		// Create files in reverse alphabetical order.
+		touch( $test_dir . 'zebra.php' );
+		touch( $test_dir . 'mango.php' );
+		touch( $test_dir . 'apple.php' );
+
+		$files = list_files( $test_dir );
+
+		unlink( $test_dir . 'zebra.php' );
+		unlink( $test_dir . 'mango.php' );
+		unlink( $test_dir . 'apple.php' );
+		rmdir( $test_dir );
+
+		$basenames = array_map( 'wp_basename', $files );
+
+		$this->assertSame( array( 'apple.php', 'mango.php', 'zebra.php' ), $basenames );
+	}
+
 	/**
 	 * Data provider.
 	 *