diff --git a/lib/class-wp-rest-global-styles-controller-gutenberg.php b/lib/class-wp-rest-global-styles-controller-gutenberg.php
index 9bbca1ffcab404..fa8bce4f5484c3 100644
--- a/lib/class-wp-rest-global-styles-controller-gutenberg.php
+++ b/lib/class-wp-rest-global-styles-controller-gutenberg.php
@@ -358,6 +358,7 @@ protected function prepare_item_for_database( $request ) {
 	 * @since 5.9.0
 	 * @since 6.2.0 Handling of style.css was added to WP_Theme_JSON.
 	 * @since 6.6.0 Added custom relative theme file URIs to `_links`.
+	 * @since 6.6.0 Added registration of custom block style variations to prevent them being stripped in response.
 	 *
 	 * @param WP_Post         $post    Global Styles post object.
 	 * @param WP_REST_Request $request Request object.
@@ -369,6 +370,29 @@ public function prepare_item_for_response( $post, $request ) { // phpcs:ignore V
 		$config                           = array();
 		$theme_json                       = null;
 		if ( $is_global_styles_user_theme_json ) {
+			if ( isset( $raw_config['styles']['blocks'] ) && is_array( $raw_config['styles']['blocks'] ) ) {
+				// Ensure custom block style variations are registered so their data isn't stripped during sanitization in WP_Theme_JSON.
+				$registry = WP_Block_Styles_Registry::get_instance();
+				foreach ( $raw_config['styles']['blocks'] as $block_name => $block_data ) {
+					if ( isset( $block_data['variations'] ) && is_array( $block_data['variations'] ) ) {
+						$registered_styles = $registry->get_registered_styles_for_block( $block_name );
+
+						foreach ( $block_data['variations'] as $variation_name => $variation_data ) {
+							// Register block style variation only if it hasn't already been registered.
+							if ( ! array_key_exists( $variation_name, $registered_styles ) ) {
+								register_block_style(
+									$block_name,
+									array(
+										'name'  => $variation_name,
+										'label' => $variation_name,
+									)
+								);
+							}
+						}
+					}
+				}
+			}
+
 			$theme_json = new WP_Theme_JSON_Gutenberg( $raw_config, 'custom' );
 			$config     = $theme_json->get_raw_data();
 		}
diff --git a/lib/experimental/kses.php b/lib/experimental/kses.php
index bed5c58697e626..18fa6c7608b58a 100644
--- a/lib/experimental/kses.php
+++ b/lib/experimental/kses.php
@@ -31,6 +31,29 @@ function gutenberg_filter_global_styles_post( $data ) {
 	) {
 		unset( $decoded_data['isGlobalStylesUserThemeJSON'] );
 
+		// Ensure block style variations are automatically registered so they will not
+		// be omitted during theme.json sanitization.
+		if ( isset( $decoded_data['styles']['blocks'] ) && is_array( $decoded_data['styles']['blocks'] ) ) {
+			$registry = WP_Block_Styles_Registry::get_instance();
+			foreach ( $decoded_data['styles']['blocks'] as $block_name => $block_data ) {
+				if ( isset( $block_data['variations'] ) && is_array( $block_data['variations'] ) ) {
+					$registered_styles = $registry->get_registered_styles_for_block( $block_name );
+
+					foreach ( $block_data['variations'] as $variation_name => $variation_data ) {
+						// Register block style variation only if it hasn't already been registered.
+						if ( ! array_key_exists( $variation_name, $registered_styles ) ) {
+							register_block_style(
+								$block_name,
+								array(
+									'name'  => $variation_name,
+									'label' => $variation_name,
+								)
+							);
+						}
+					}
+				}
+			}
+		}
 		$data_to_encode = WP_Theme_JSON_Gutenberg::remove_insecure_properties( $decoded_data );
 
 		$data_to_encode['isGlobalStylesUserThemeJSON'] = true;
diff --git a/phpunit/class-wp-rest-global-styles-controller-gutenberg-test.php b/phpunit/class-wp-rest-global-styles-controller-gutenberg-test.php
index f5b216a084a4c9..ff5b291b2f315b 100644
--- a/phpunit/class-wp-rest-global-styles-controller-gutenberg-test.php
+++ b/phpunit/class-wp-rest-global-styles-controller-gutenberg-test.php
@@ -513,6 +513,39 @@ public function test_update_item_invalid_styles_css() {
 		$this->assertErrorResponse( 'rest_custom_css_illegal_markup', $response, 400 );
 	}
 
+	/**
+	 * @covers WP_REST_Global_Styles_Controller_Gutenberg::update_item
+	 */
+	public function test_update_item_with_custom_block_style_variations() {
+		wp_set_current_user( self::$admin_id );
+		if ( is_multisite() ) {
+			grant_super_admin( self::$admin_id );
+		}
+		$variations = array(
+			'dark' => array(
+				'color' => array(
+					'background' => '#000000',
+					'text'       => '#ffffff',
+				),
+			),
+		);
+		$request    = new WP_REST_Request( 'PUT', '/wp/v2/global-styles/' . self::$global_styles_id );
+		$request->set_body_params(
+			array(
+				'styles' => array(
+					'blocks' => array(
+						'core/group' => array(
+							'variations' => $variations,
+						),
+					),
+				),
+			)
+		);
+		$response = rest_get_server()->dispatch( $request );
+		$data     = $response->get_data();
+		$this->assertSame( $variations, $data['styles']['blocks']['core/group']['variations'] );
+	}
+
 	/**
 	 * @doesNotPerformAssertions
 	 */