diff --git a/django/db/models/sql/query.py b/django/db/models/sql/query.py
index 4f2fe5acb5..74aed551a3 100644
--- a/django/db/models/sql/query.py
+++ b/django/db/models/sql/query.py
@@ -22,7 +22,7 @@ from django.db import DEFAULT_DB_ALIAS, NotSupportedError, connections
 from django.db.models.aggregates import Count
 from django.db.models.constants import LOOKUP_SEP
 from django.db.models.expressions import (
-    BaseExpression, Col, F, OuterRef, Ref, SimpleCol,
+    BaseExpression, Col, F, OuterRef, Ref, SimpleCol, Subquery,
 )
 from django.db.models.fields import Field
 from django.db.models.fields.related_lookups import MultiColSource
@@ -382,7 +382,7 @@ class Query(BaseExpression):
                 # before the contains_aggregate/is_summary condition below.
                 new_expr, col_cnt = self.rewrite_cols(expr, col_cnt)
                 new_exprs.append(new_expr)
-            elif isinstance(expr, Col) or (expr.contains_aggregate and not expr.is_summary):
+            elif isinstance(expr, (Col, Subquery)) or (expr.contains_aggregate and not expr.is_summary):
                 # Reference to column. Make sure the referenced column
                 # is selected.
                 col_cnt += 1
diff --git a/tests/expressions/tests.py b/tests/expressions/tests.py
index cc03e83ff4..bb448745c8 100644
--- a/tests/expressions/tests.py
+++ b/tests/expressions/tests.py
@@ -551,6 +551,19 @@ class BasicExpressionsTests(TestCase):
         )
         self.assertEqual(qs.get().float, 1.2)
 
+    @skipUnlessDBFeature('supports_subqueries_in_group_by')
+    def test_aggregate_subquery_annotation(self):
+        aggregate = Company.objects.annotate(
+            ceo_salary=Subquery(
+                Employee.objects.filter(
+                    id=OuterRef('ceo_id'),
+                ).values('salary')
+            ),
+        ).aggregate(
+            ceo_salary_gt_20=Count('pk', filter=Q(ceo_salary__gt=20)),
+        )
+        self.assertEqual(aggregate, {'ceo_salary_gt_20': 1})
+
     def test_explicit_output_field(self):
         class FuncA(Func):
             output_field = models.CharField()