diff --git a/packages/grafana-data/src/transformations/transformers/joinDataFrames.test.ts b/packages/grafana-data/src/transformations/transformers/joinDataFrames.test.ts
index 976ea8fd731..0515131be30 100644
--- a/packages/grafana-data/src/transformations/transformers/joinDataFrames.test.ts
+++ b/packages/grafana-data/src/transformations/transformers/joinDataFrames.test.ts
@@ -280,6 +280,65 @@ describe('align frames', () => {
         ]
       `);
     });
+
+    it('should perform an inner join with empty values', () => {
+      const out = joinDataFrames({
+        frames: [
+          toDataFrame({
+            fields: [
+              {
+                name: 'A',
+                type: FieldType.string,
+                values: [],
+              },
+              {
+                name: 'B',
+                type: FieldType.string,
+                values: [],
+              },
+            ],
+          }),
+          toDataFrame({
+            fields: [
+              {
+                name: 'A',
+                type: FieldType.string,
+                values: [],
+              },
+              {
+                name: 'C',
+                type: FieldType.string,
+                values: [],
+              },
+            ],
+          }),
+        ],
+        joinBy: fieldMatchers.get(FieldMatcherID.byName).get('A'),
+        mode: JoinMode.inner,
+      })!;
+
+      expect(
+        out.fields.map((f) => ({
+          name: f.name,
+          values: f.values,
+        }))
+      ).toMatchInlineSnapshot(`
+        [
+          {
+            "name": "A",
+            "values": [],
+          },
+          {
+            "name": "B",
+            "values": [],
+          },
+          {
+            "name": "C",
+            "values": [],
+          },
+        ]
+      `);
+    });
   });
 
   it('unsorted input keep indexes', () => {
diff --git a/packages/grafana-data/src/transformations/transformers/joinDataFrames.ts b/packages/grafana-data/src/transformations/transformers/joinDataFrames.ts
index a2e5f0ad080..6f8f592f36c 100644
--- a/packages/grafana-data/src/transformations/transformers/joinDataFrames.ts
+++ b/packages/grafana-data/src/transformations/transformers/joinDataFrames.ts
@@ -424,7 +424,8 @@ function joinInner(tables: AlignedData[]): Array<Array<string | number | null |
 
   // Check if joinedTables is empty before transposing. No need to transpose if there are no joined tables.
   if (joinedTables.length === 0) {
-    return [];
+    const fieldCount = tables.reduce((count, table) => count + (table.length - 1), 1);
+    return Array.from({ length: fieldCount }, () => []);
   }
 
   // Transpose the joined tables to get the desired output format.