diff --git a/src/CP/Navigation/NavTransformer.php b/src/CP/Navigation/NavTransformer.php
index 2f1f8001ebc..c90ad400d6a 100644
--- a/src/CP/Navigation/NavTransformer.php
+++ b/src/CP/Navigation/NavTransformer.php
@@ -281,6 +281,30 @@ protected function getReorderedItems($originalList, $newList): bool|array
      */
     protected function calculateMinimumItemsForReorder($originalList, $newList): int
     {
+        // When the new list contains items not in the original (e.g., custom sections),
+        // we need to include enough items to establish where those new items are positioned,
+        // BUT only if they appear in the middle of the list. Items appended at the end
+        // don't need to be explicitly positioned.
+
+        $originalSet = collect($originalList);
+        $lastCustomPositionInMiddle = 0;
+
+        foreach ($newList as $index => $item) {
+            if (! $originalSet->contains($item)) {
+                // Check if there are any original items after this custom item
+                $hasOriginalItemsAfter = collect($newList)
+                    ->slice($index + 1)
+                    ->contains(fn ($futureItem) => $originalSet->contains($futureItem));
+
+                // Only track this position if there are original items after it
+                // (meaning it's in the middle, not at the end)
+                if ($hasOriginalItemsAfter) {
+                    $lastCustomPositionInMiddle = $index + 1;
+                }
+            }
+        }
+
+        // Use the original algorithm for reordering existing items
         $continueRejecting = true;
 
         $minimumItemsCount = collect($originalList)
@@ -295,7 +319,11 @@ protected function calculateMinimumItemsForReorder($originalList, $newList): int
             })
             ->count();
 
-        return max(1, $minimumItemsCount - 1);
+        $minimumFromReordering = max(1, $minimumItemsCount - 1);
+
+        // If we have custom items in the middle of the list, we need to include
+        // enough items to establish their position. Return the maximum of the two.
+        return max($minimumFromReordering, $lastCustomPositionInMiddle);
     }
 
     /**
@@ -329,7 +357,7 @@ protected function minify()
             ->values()
             ->all();
 
-        $this->config = $reorder
+        $this->config = ! empty($reorder)
             ? array_filter(compact('reorder', 'sections'))
             : $sections;
 
diff --git a/tests/CP/Navigation/NavTransformerTest.php b/tests/CP/Navigation/NavTransformerTest.php
index fa867884bbc..54c1a629f4b 100644
--- a/tests/CP/Navigation/NavTransformerTest.php
+++ b/tests/CP/Navigation/NavTransformerTest.php
@@ -1315,6 +1315,60 @@ public function it_can_transform_complex_json_payload_copied_from_actual_vue_sub
 
         $this->assertEquals($expected, $transformed);
     }
+
+    #[Test]
+    public function it_preserves_reorder_array_when_moving_custom_section_to_first_position()
+    {
+        // This test reproduces a bug where moving a custom section to the first position
+        // (after "Top Level") results in the reorder array being dropped during the minifying
+        // process, even though it is necessary to maintain the custom section's position.
+
+        $transformed = $this->transform([
+            ['display_original' => 'Top Level'],
+            [
+                'display' => '⭐ Favorites',
+                'action' => '@create',
+                'items' => [
+                    [
+                        'id' => 'favorites::edit_homepage',
+                        'manipulations' => [
+                            'action' => '@create',
+                            'display' => 'Edit homepage',
+                            'url' => '/cp',
+                            'icon' => 'edit',
+                        ],
+                    ],
+                ],
+            ],
+            ['display_original' => 'Content'],
+            ['display_original' => 'Fields'],
+            ['display_original' => 'Tools'],
+            ['display_original' => 'Settings'],
+            ['display_original' => 'Users'],
+        ]);
+
+        $expected = [
+            'reorder' => [
+                'favorites',
+            ],
+            'sections' => [
+                'favorites' => [
+                    'display' => '⭐ Favorites',
+                    'action' => '@create',
+                    'items' => [
+                        'favorites::edit_homepage' => [
+                            'action' => '@create',
+                            'display' => 'Edit homepage',
+                            'url' => '/cp',
+                            'icon' => 'edit',
+                        ],
+                    ],
+                ],
+            ],
+        ];
+
+        $this->assertEquals($expected, $transformed);
+    }
 }
 
 class IncrementalIdHasher