diff --git a/codegen/config/config.go b/codegen/config/config.go
index 72525401f96..1638239d003 100644
--- a/codegen/config/config.go
+++ b/codegen/config/config.go
@@ -185,9 +185,35 @@ func (c *Config) Check() error {
 		}
 	}
 
+	// check packages names against conflict, if present in the same dir
+	// and check filenames for uniqueness
+	packageConfigList := []PackageConfig{
+		c.Model,
+		c.Exec,
+		c.Resolver,
+	}
+	filesMap := make(map[string]bool)
+	pkgConfigsByDir := make(map[string]PackageConfig)
+	for _, current := range packageConfigList {
+		_, fileFound := filesMap[current.Filename]
+		if fileFound {
+			return fmt.Errorf("filename %s defined more than once", current.Filename)
+		}
+		filesMap[current.Filename] = true
+		previous, inSameDir := pkgConfigsByDir[current.Dir()]
+		if inSameDir && current.Package != previous.Package {
+			return fmt.Errorf("filenames %s and %s are in the same directory but have different package definitions", stripPath(current.Filename), stripPath(previous.Filename))
+		}
+		pkgConfigsByDir[current.Dir()] = current
+	}
+
 	return c.normalize()
 }
 
+func stripPath(path string) string {
+	return filepath.Base(path)
+}
+
 type TypeMap map[string]TypeMapEntry
 
 func (tm TypeMap) Exists(typeName string) bool {
diff --git a/codegen/config/config_test.go b/codegen/config/config_test.go
index 3f6ee668ac7..d4f94f9c973 100644
--- a/codegen/config/config_test.go
+++ b/codegen/config/config_test.go
@@ -78,3 +78,16 @@ func TestReferencedPackages(t *testing.T) {
 	})
 
 }
+
+func TestConfigCheck(t *testing.T) {
+	t.Run("invalid config format due to conflicting package names", func(t *testing.T) {
+		config, err := LoadConfig("testdata/cfg/conflictedPackages.yml")
+		require.NoError(t, err)
+
+		err = config.normalize()
+		require.NoError(t, err)
+
+		err = config.check()
+		require.EqualError(t, err, "filenames exec.go and models.go are in the same directory but have different package definitions")
+	})
+}
diff --git a/codegen/testdata/cfg/conflictedPackages.yml b/codegen/testdata/cfg/conflictedPackages.yml
new file mode 100644
index 00000000000..ec6ceea515a
--- /dev/null
+++ b/codegen/testdata/cfg/conflictedPackages.yml
@@ -0,0 +1,10 @@
+schema:
+  - schema.graphql
+exec:
+  filename: generated/exec.go
+  package: graphql
+model:
+  filename: generated/models.go
+resolver:
+  filename: generated/resolver.go
+  type: Resolver
diff --git a/plugin/modelgen/testdata/gqlgen.yml b/plugin/modelgen/testdata/gqlgen.yml
index b32289be0d3..9c01c79b685 100644
--- a/plugin/modelgen/testdata/gqlgen.yml
+++ b/plugin/modelgen/testdata/gqlgen.yml
@@ -2,7 +2,7 @@ schema:
   - "testdata/schema.graphql"
 
 exec:
-  filename: out/generated.go
+  filename: out/ignored.go
 model:
   filename: out/generated.go