diff --git a/public/lib/db/upgrade.php b/public/lib/db/upgrade.php
index 9d7ae1af279..e1e365a7b84 100644
--- a/public/lib/db/upgrade.php
+++ b/public/lib/db/upgrade.php
@@ -2385,5 +2385,11 @@ function xmldb_main_upgrade($oldversion) {
         upgrade_main_savepoint(true, 2025100601.04);
     }
 
+    if ($oldversion < 2025100601.06) {
+        \core_question\category_manager::fix_restored_category_parents();
+        // Main savepoint reached.
+        upgrade_main_savepoint(true, 2025100601.06);
+    }
+
     return true;
 }
diff --git a/public/question/classes/category_manager.php b/public/question/classes/category_manager.php
index 1138e69cb12..10fe2368c69 100644
--- a/public/question/classes/category_manager.php
+++ b/public/question/classes/category_manager.php
@@ -377,4 +377,30 @@ class category_manager {
         $lastmax = $DB->get_field_sql($sql, ['parent' => $parentid]);
         return $lastmax ?? 0;
     }
+
+    /**
+     * Upgrade step to find question categories with the wrong parent category.
+     *
+     * This will find question categories that have a parent in a different context, and set the parent to the top category
+     * of the current context. GROUP BY is to ensure we only get one result for each category, just in case we somehow end up
+     * with multiple top-level categories in a context.
+     *
+     * This could occur before the fix for MDL-86300, where a course restore left question categories that were the child of a top
+     * category with the original top category as the parent, rather than the new top category.
+     *
+     * This only needs to one once on upgrade, so is deprecated for removal in 6.0.
+     */
+    public static function fix_restored_category_parents(): void {
+        global $DB;
+        $categoriestofix = $DB->get_records_sql("
+            SELECT qc.id as id, MIN(qc3.id) AS parent
+              FROM {question_categories} qc
+              JOIN {question_categories} qc2 ON qc2.id = qc.parent AND qc.contextid != qc2.contextid
+              JOIN {question_categories} qc3 ON qc3.contextid = qc.contextid AND qc3.parent = 0
+          GROUP BY qc.id
+        ");
+        foreach ($categoriestofix as $categorytofix) {
+            $DB->update_record('question_categories', $categorytofix, true);
+        }
+    }
 }
diff --git a/public/question/tests/category_manager_test.php b/public/question/tests/category_manager_test.php
index 4d33ddcb183..a8354ccdb82 100644
--- a/public/question/tests/category_manager_test.php
+++ b/public/question/tests/category_manager_test.php
@@ -605,4 +605,63 @@ final class category_manager_test extends \advanced_testcase {
         $questiongenerator->create_question_category(['contextid' => $context->id, 'parent' => $qcategory2->id]);
         $this->assertEquals(1, $manager->get_max_sortorder($qcategory2->id));
     }
+
+    /**
+     * Check that question categories with the wrong parent are fixed.
+     */
+    public function test_fix_restored_category_parents(): void {
+        global $CFG, $DB, $USER;
+        require_once($CFG->dirroot . '/backup/util/includes/backup_includes.php');
+
+        $this->resetAfterTest();
+        $this->setAdminUser();
+
+        // Create a course.
+        $generator = $this->getDataGenerator();
+        $course = $generator->create_course();
+
+        // Add 2 quizzes with question categories.
+        $quiz1 = $generator->create_module('quiz', ['course' => $course->id]);
+        $quiz1context = \context_module::instance($quiz1->cmid);
+        $quiz1top = question_get_top_category($quiz1context->id);
+        $quiz1questioncats = $DB->get_records('question_categories', ['contextid' => $quiz1context->id]);
+        $this->assertCount(2, $quiz1questioncats);
+
+        $quiz2 = $generator->create_module('quiz', ['course' => $course->id]);
+        $quiz2context = \context_module::instance($quiz2->cmid);
+        $quiz2top = question_get_top_category($quiz2context->id);
+        $quiz2questioncats = $DB->get_records('question_categories', ['contextid' => $quiz2context->id]);
+        $this->assertCount(2, $quiz2questioncats);
+
+        // Add 2 question banks with question categories.
+        $qbank1 = $this->getDataGenerator()->create_module('qbank', ['course' => $course->id]);
+        $qbank1context = \context_module::instance($qbank1->cmid);
+        $qbank1top = question_get_top_category($qbank1context->id);
+        $qbank1questioncats = $DB->get_records('question_categories', ['contextid' => $qbank1context->id]);
+        $this->assertCount(2, $qbank1questioncats);
+
+        $qbank2 = $this->getDataGenerator()->create_module('qbank', ['course' => $course->id]);
+        $qbank2context = \context_module::instance($qbank2->cmid);
+        $qbank2top = question_get_top_category($qbank2context->id);
+        $qbank2questioncats = $DB->get_records('question_categories', ['contextid' => $qbank2context->id]);
+        $this->assertCount(2, $qbank2questioncats);
+
+        // Modify the child question categories of the second quiz and qbank instances so they are children of the
+        // first instances' top categories.
+        $quiz2nontop = question_get_default_category($quiz2context->id);
+        $DB->set_field('question_categories', 'parent', $quiz1top->id, ['id' => $quiz2nontop->id]);
+
+        $qbank2nontop = question_get_default_category($qbank2context->id);
+        $DB->set_field('question_categories', 'parent', $qbank1top->id, ['id' => $qbank2nontop->id]);
+
+        $this->assertEquals($quiz1top->id, $DB->get_field('question_categories', 'parent', ['id' => $quiz2nontop->id]));
+        $this->assertEquals($qbank1top->id, $DB->get_field('question_categories', 'parent', ['id' => $qbank2nontop->id]));
+
+        // Run the fix.
+        category_manager::fix_restored_category_parents();
+
+        // Check that the child categories now have the correct parents.
+        $this->assertEquals($quiz2top->id, $DB->get_field('question_categories', 'parent', ['id' => $quiz2nontop->id]));
+        $this->assertEquals($qbank2top->id, $DB->get_field('question_categories', 'parent', ['id' => $qbank2nontop->id]));
+    }
 }
diff --git a/public/version.php b/public/version.php
index 4b2f12e19f5..08428584489 100644
--- a/public/version.php
+++ b/public/version.php
@@ -29,7 +29,7 @@
 
 defined('MOODLE_INTERNAL') || die();
 
-$version  = 2025100601.05;              // 20251006      = branching date YYYYMMDD - do not modify!
+$version  = 2025100601.06;              // 20251006      = branching date YYYYMMDD - do not modify!
                                         //         RR    = release increments - 00 in DEV branches.
                                         //           .XX = incremental changes.
 $release  = '5.1.1+ (Build: 20260109)';    // Human-friendly version name