diff --git a/app/models/merge_request.rb b/app/models/merge_request.rb
index 2035bffd829..790555ab045 100644
--- a/app/models/merge_request.rb
+++ b/app/models/merge_request.rb
@@ -1322,7 +1322,7 @@ class MergeRequest < ActiveRecord::Base
   def base_pipeline
     @base_pipeline ||= project.ci_pipelines
       .order(id: :desc)
-      .find_by(sha: diff_base_sha)
+      .find_by(sha: diff_base_sha, ref: target_branch)
   end
 
   def discussions_rendered_on_frontend?
diff --git a/changelogs/unreleased/57671-fix_merge_request_base_pipeline.yml b/changelogs/unreleased/57671-fix_merge_request_base_pipeline.yml
new file mode 100644
index 00000000000..d89819eee60
--- /dev/null
+++ b/changelogs/unreleased/57671-fix_merge_request_base_pipeline.yml
@@ -0,0 +1,5 @@
+---
+title: Ensure the base pipeline of a Merge Request belongs to its target branch
+merge_request: 25226
+author:
+type: fixed
diff --git a/spec/models/merge_request_spec.rb b/spec/models/merge_request_spec.rb
index afa87b8a62d..fbd19b024a0 100644
--- a/spec/models/merge_request_spec.rb
+++ b/spec/models/merge_request_spec.rb
@@ -2604,8 +2604,9 @@ describe MergeRequest do
 
     let!(:first_pipeline) { create(:ci_pipeline_without_jobs, pipeline_arguments) }
     let!(:last_pipeline) { create(:ci_pipeline_without_jobs, pipeline_arguments) }
+    let!(:last_pipeline_with_other_ref) { create(:ci_pipeline_without_jobs, pipeline_arguments.merge(ref: 'other')) }
 
-    it 'returns latest pipeline' do
+    it 'returns latest pipeline for the target branch' do
       expect(merge_request.base_pipeline).to eq(last_pipeline)
     end
   end