diff --git a/src/wp-includes/theme.php b/src/wp-includes/theme.php
index f063bc97a0f84..81c91ab5cc8a5 100644
--- a/src/wp-includes/theme.php
+++ b/src/wp-includes/theme.php
@@ -840,6 +840,13 @@ function switch_theme( $stylesheet ) {
 	$new_theme->delete_pattern_cache();
 	$old_theme->delete_pattern_cache();
 
+	// Set autoload=no for the old theme, autoload=yes for the switched theme.
+	$theme_mods_options = array(
+		'theme_mods_' . $stylesheet                  => 'yes',
+		'theme_mods_' . $old_theme->get_stylesheet() => 'no',
+	);
+	wp_set_option_autoload_values( $theme_mods_options );
+
 	/**
 	 * Fires after the theme is switched.
 	 *
diff --git a/tests/phpunit/tests/theme/autoloadThemeMods.php b/tests/phpunit/tests/theme/autoloadThemeMods.php
new file mode 100644
index 0000000000000..e653ac6a77a84
--- /dev/null
+++ b/tests/phpunit/tests/theme/autoloadThemeMods.php
@@ -0,0 +1,42 @@
+<?php
+
+require_once __DIR__ . '/base.php';
+
+/**
+ * Test autoload for theme mods.
+ *
+ * @package WordPress
+ * @subpackage Theme
+ *
+ * @group themes
+ */
+class Tests_Autoload_Theme_Mods extends WP_Theme_UnitTestCase {
+
+	/**
+	 * Tests that theme mods should not autoloaded after switch_theme.
+	 *
+	 * @ticket 39537
+	 */
+	public function test_that_on_switch_theme_previous_theme_mods_should_not_be_autoload() {
+		global $wpdb;
+
+		$current_theme_stylesheet = get_stylesheet();
+
+		// Set a theme mod for the current theme.
+		$new_theme_stylesheet = 'block-theme';
+		set_theme_mod( 'foo-bar-option', 'a-value' );
+
+		switch_theme( $new_theme_stylesheet );
+
+		$this->assertSame( 'no', $wpdb->get_var( $wpdb->prepare( "SELECT autoload FROM $wpdb->options WHERE option_name = %s", "theme_mods_$current_theme_stylesheet" ) ), 'Theme mods autoload value not set to no in database' );
+		$this->assertSame( 'yes', $wpdb->get_var( $wpdb->prepare( "SELECT autoload FROM $wpdb->options WHERE option_name = %s", "theme_mods_$new_theme_stylesheet" ) ), 'Theme mods autoload value not set to yes in database' );
+
+		switch_theme( $current_theme_stylesheet );
+
+		$this->assertSame( 'yes', $wpdb->get_var( $wpdb->prepare( "SELECT autoload FROM $wpdb->options WHERE option_name = %s", "theme_mods_$current_theme_stylesheet" ) ), 'Theme mods autoload value not set to yes in database' );
+		$this->assertSame( 'no', $wpdb->get_var( $wpdb->prepare( "SELECT autoload FROM $wpdb->options WHERE option_name = %s", "theme_mods_$new_theme_stylesheet" ) ), 'Theme mods autoload value not set to no in database' );
+
+		// Basic assertion to make sure that we haven't lost the mods.
+		$this->assertSame( 'a-value', get_theme_mod( 'foo-bar-option' ) );
+	}
+}