diff --git a/src/wp-includes/query.php b/src/wp-includes/query.php
index c38a11c083..27d8c26fa4 100644
--- a/src/wp-includes/query.php
+++ b/src/wp-includes/query.php
@@ -3900,15 +3900,17 @@ class WP_Query {
 				// For other tax queries, grab the first term from the first clause.
 				$tax_query_in_and = wp_list_filter( $this->tax_query->queried_terms, array( 'operator' => 'NOT IN' ), 'NOT' );
 
-				$queried_taxonomies = array_keys( $tax_query_in_and );
-				$matched_taxonomy = reset( $queried_taxonomies );
-				$query = $tax_query_in_and[ $matched_taxonomy ];
+				if ( ! empty( $tax_query_in_and ) ) {
+					$queried_taxonomies = array_keys( $tax_query_in_and );
+					$matched_taxonomy = reset( $queried_taxonomies );
+					$query = $tax_query_in_and[ $matched_taxonomy ];
 
-				if ( $query['terms'] ) {
-					if ( 'term_id' == $query['field'] ) {
-						$term = get_term( reset( $query['terms'] ), $matched_taxonomy );
-					} else {
-						$term = get_term_by( $query['field'], reset( $query['terms'] ), $matched_taxonomy );
+					if ( $query['terms'] ) {
+						if ( 'term_id' == $query['field'] ) {
+							$term = get_term( reset( $query['terms'] ), $matched_taxonomy );
+						} else {
+							$term = get_term_by( $query['field'], reset( $query['terms'] ), $matched_taxonomy );
+						}
 					}
 				}
 			}
diff --git a/tests/phpunit/tests/query.php b/tests/phpunit/tests/query.php
index 3217ac5c37..c1aa6df309 100644
--- a/tests/phpunit/tests/query.php
+++ b/tests/phpunit/tests/query.php
@@ -91,4 +91,35 @@ class Tests_Query extends WP_UnitTestCase {
 		$this->assertCount( 1, $query->get( 'tag_slug__in' ) );
 		$this->assertEquals( $query->get_queried_object(), $tag );
 	}
-}
\ No newline at end of file
+
+	/**
+	 * @ticket 31246
+	 */
+	public function test_get_queried_object_should_return_null_when_is_tax_is_true_but_the_taxonomy_args_have_been_removed_in_a_parse_query_callback() {
+		// Don't override the args provided below.
+		remove_action( 'pre_get_posts', array( $this, 'pre_get_posts_tax_category_tax_query' ) );
+		register_taxonomy( 'wptests_tax', 'post' );
+		$terms = $this->factory->term->create_many( 2, array(
+			'taxonomy' => 'wptests_tax',
+		) );
+
+		$posts = $this->factory->post->create_many( 2 );
+
+		wp_set_object_terms( $posts[0], array( $terms[0] ), 'wptests_tax' );
+		wp_set_object_terms( $posts[1], array( $terms[1] ), 'wptests_tax' );
+
+		add_action( 'parse_query', array( $this, 'filter_parse_query_to_remove_tax' ) );
+		$q = new WP_Query( array(
+			'fields' => 'ids',
+			'wptests_tax' => $terms[1],
+		) );
+
+		remove_action( 'parse_query', array( $this, 'filter_parse_query_to_remove_tax' ) );
+
+		$this->assertNull( $q->get_queried_object() );
+	}
+
+	public function filter_parse_query_to_remove_tax( $q ) {
+		unset( $q->query_vars['wptests_tax'] );
+	}
+}