diff --git a/changelog/fix_rubocop_todo_link_injection_when.md b/changelog/fix_rubocop_todo_link_injection_when.md
new file mode 100644
index 000000000000..5bc127914498
--- /dev/null
+++ b/changelog/fix_rubocop_todo_link_injection_when.md
@@ -0,0 +1 @@
+* [#9406](https://github.com/rubocop-hq/rubocop/pull/9406): Fix rubocop_todo link injection when YAML doc start sigil exists. ([@dduugg][])
diff --git a/lib/rubocop/cli/command/auto_genenerate_config.rb b/lib/rubocop/cli/command/auto_genenerate_config.rb
index aa60e02043d6..f0586fec98dc 100644
--- a/lib/rubocop/cli/command/auto_genenerate_config.rb
+++ b/lib/rubocop/cli/command/auto_genenerate_config.rb
@@ -9,6 +9,7 @@ class AutoGenerateConfig < Base
         self.command_name = :auto_gen_config
 
         AUTO_GENERATED_FILE = '.rubocop_todo.yml'
+        YAML_OPTIONAL_DOC_START = /\A---(\s+#|\s*\z)/.freeze
 
         PHASE_1 = 'Phase 1 of 2: run Layout/LineLength cop'
         PHASE_2 = 'Phase 2 of 2: run all cops'
@@ -130,10 +131,10 @@ def existing_configuration(config_file)
         end
 
         def write_config_file(file_name, file_string, rubocop_yml_contents)
-          File.open(file_name, 'w') do |f|
-            f.write "inherit_from:#{file_string}\n"
-            f.write "\n#{rubocop_yml_contents}" if /\S/.match?(rubocop_yml_contents)
-          end
+          lines = /\S/.match?(rubocop_yml_contents) ? rubocop_yml_contents.split("\n", -1) : []
+          doc_start_index = lines.index { |line| YAML_OPTIONAL_DOC_START.match?(line) } || -1
+          lines.insert(doc_start_index + 1, "inherit_from:#{file_string}\n")
+          File.open(file_name, 'w') { |f| f.write lines.join("\n") }
         end
       end
     end
diff --git a/spec/rubocop/cli/cli_auto_gen_config_spec.rb b/spec/rubocop/cli/cli_auto_gen_config_spec.rb
index 99c8903c5f8c..69fb3e91fd00 100644
--- a/spec/rubocop/cli/cli_auto_gen_config_spec.rb
+++ b/spec/rubocop/cli/cli_auto_gen_config_spec.rb
@@ -482,6 +482,43 @@ def fooBar; end
       end
     end
 
+    context 'when existing config file has a YAML document start header' do
+      it 'inserts `inherit_from` key after hearder' do
+        create_file('example1.rb', <<~RUBY)
+          def foo; end
+        RUBY
+        create_file('.rubocop.yml', <<~YAML)
+          # rubocop config file
+          ---  # YAML document start
+          # The following cop does not support auto-correction.
+          Naming/MethodName:
+            Enabled: true
+        YAML
+        expect(cli.run(%w[--auto-gen-config])).to eq(0)
+        expect($stderr.string).to eq('')
+        expect(Dir['.*']).to include('.rubocop_todo.yml')
+        todo_contents = IO.read('.rubocop_todo.yml').lines[8..-1].join
+        expect(todo_contents).to eq(<<~YAML)
+          # Offense count: 1
+          # Cop supports --auto-correct.
+          # Configuration parameters: EnforcedStyle.
+          # SupportedStyles: always, always_true, never
+          Style/FrozenStringLiteralComment:
+            Exclude:
+              - 'example1.rb'
+        YAML
+        expect(IO.read('.rubocop.yml')).to eq(<<~YAML)
+          # rubocop config file
+          ---  # YAML document start
+          inherit_from: .rubocop_todo.yml
+
+          # The following cop does not support auto-correction.
+          Naming/MethodName:
+            Enabled: true
+        YAML
+      end
+    end
+
     context 'when working in a subdirectory' do
       it 'can generate a todo list' do
         create_file('dir/example1.rb', ['$x = 0 ',