diff --git a/django/contrib/admin/checks.py b/django/contrib/admin/checks.py
index 2c90dedc3129a..45d895dff066e 100644
--- a/django/contrib/admin/checks.py
+++ b/django/contrib/admin/checks.py
@@ -533,6 +533,16 @@ def _check_filter_item(self, obj, field_name, label):
                 return must_be(
                     "a many-to-many field", option=label, obj=obj, id="admin.E020"
                 )
+            elif not field.remote_field.through._meta.auto_created:
+                return [
+                    checks.Error(
+                        f"The value of '{label}' cannot include the ManyToManyField "
+                        f"'{field_name}', because that field manually specifies a "
+                        f"relationship model.",
+                        obj=obj.__class__,
+                        id="admin.E013",
+                    )
+                ]
             else:
                 return []
 
diff --git a/docs/ref/checks.txt b/docs/ref/checks.txt
index 50f7c1b166b6f..de7b0dc382990 100644
--- a/docs/ref/checks.txt
+++ b/docs/ref/checks.txt
@@ -637,9 +637,10 @@ with the admin site:
 * **admin.E011**: The value of ``fieldsets[n][1]`` must contain the key
   ``fields``.
 * **admin.E012**: There are duplicate field(s) in ``fieldsets[n][1]``.
-* **admin.E013**: The value of ``fields[n]/fieldsets[n][m]`` cannot include the
-  ``ManyToManyField`` ``<field name>``, because that field manually specifies a
-  relationship model.
+* **admin.E013**: The value of
+  ``fields[n]/filter_horizontal[n]/filter_vertical[n]/fieldsets[n][m]`` cannot
+  include the ``ManyToManyField`` ``<field name>``, because that field manually
+  specifies a relationship model.
 * **admin.E014**: The value of ``exclude`` must be a list or tuple.
 * **admin.E015**: The value of ``exclude`` contains duplicate field(s).
 * **admin.E016**: The value of ``form`` must inherit from ``BaseModelForm``.
diff --git a/tests/modeladmin/test_checks.py b/tests/modeladmin/test_checks.py
index 69aa242a64039..2ed27f8a3dde3 100644
--- a/tests/modeladmin/test_checks.py
+++ b/tests/modeladmin/test_checks.py
@@ -4,10 +4,11 @@
 from django.contrib.admin.options import VERTICAL, ModelAdmin, TabularInline
 from django.contrib.admin.sites import AdminSite
 from django.core.checks import Error
-from django.db.models import CASCADE, F, Field, ForeignKey, Model
+from django.db.models import CASCADE, F, Field, ForeignKey, ManyToManyField, Model
 from django.db.models.functions import Upper
 from django.forms.models import BaseModelFormSet
 from django.test import SimpleTestCase
+from django.test.utils import isolate_apps
 
 from .models import Band, Song, User, ValidationTestInlineModel, ValidationTestModel
 
@@ -321,6 +322,26 @@ class TestModelAdmin(ModelAdmin):
             "admin.E020",
         )
 
+    @isolate_apps("modeladmin")
+    def test_invalid_m2m_field_with_through(self):
+        class Artist(Model):
+            bands = ManyToManyField("Band", through="BandArtist")
+
+        class BandArtist(Model):
+            artist = ForeignKey("Artist", on_delete=CASCADE)
+            band = ForeignKey("Band", on_delete=CASCADE)
+
+        class TestModelAdmin(ModelAdmin):
+            filter_vertical = ["bands"]
+
+        self.assertIsInvalid(
+            TestModelAdmin,
+            Artist,
+            "The value of 'filter_vertical[0]' cannot include the ManyToManyField "
+            "'bands', because that field manually specifies a relationship model.",
+            "admin.E013",
+        )
+
     def test_valid_case(self):
         class TestModelAdmin(ModelAdmin):
             filter_vertical = ("users",)
@@ -363,6 +384,26 @@ class TestModelAdmin(ModelAdmin):
             "admin.E020",
         )
 
+    @isolate_apps("modeladmin")
+    def test_invalid_m2m_field_with_through(self):
+        class Artist(Model):
+            bands = ManyToManyField("Band", through="BandArtist")
+
+        class BandArtist(Model):
+            artist = ForeignKey("Artist", on_delete=CASCADE)
+            band = ForeignKey("Band", on_delete=CASCADE)
+
+        class TestModelAdmin(ModelAdmin):
+            filter_horizontal = ["bands"]
+
+        self.assertIsInvalid(
+            TestModelAdmin,
+            Artist,
+            "The value of 'filter_horizontal[0]' cannot include the ManyToManyField "
+            "'bands', because that field manually specifies a relationship model.",
+            "admin.E013",
+        )
+
     def test_valid_case(self):
         class TestModelAdmin(ModelAdmin):
             filter_horizontal = ("users",)