diff --git a/app/services/delete_merged_branches_service.rb b/app/services/delete_merged_branches_service.rb
index 1b5623baebe..3b611588466 100644
--- a/app/services/delete_merged_branches_service.rb
+++ b/app/services/delete_merged_branches_service.rb
@@ -8,9 +8,20 @@ class DeleteMergedBranchesService < BaseService
 
     branches = project.repository.branch_names
     branches = branches.select { |branch| project.repository.merged_to_root_ref?(branch) }
+    # Prevent deletion of branches relevant to open merge requests
+    branches -= merge_request_branch_names
 
     branches.each do |branch|
       DeleteBranchService.new(project, current_user).execute(branch)
     end
   end
+
+  private
+
+  def merge_request_branch_names
+    # reorder(nil) is necessary for SELECT DISTINCT because default scope adds an ORDER BY
+    source_names = project.origin_merge_requests.opened.reorder(nil).uniq.pluck(:source_branch)
+    target_names = project.merge_requests.opened.reorder(nil).uniq.pluck(:target_branch)
+    (source_names + target_names).uniq
+  end
 end
diff --git a/changelogs/unreleased/sh-issue-29247-fix.yml b/changelogs/unreleased/sh-issue-29247-fix.yml
new file mode 100644
index 00000000000..b530e5da55b
--- /dev/null
+++ b/changelogs/unreleased/sh-issue-29247-fix.yml
@@ -0,0 +1,5 @@
+---
+title: Don't delete a branch involved in an open merge request in "Delete all merged
+  branches" service
+merge_request:
+author:
diff --git a/spec/factories/merge_requests.rb b/spec/factories/merge_requests.rb
index 361f9dac191..253a025af48 100644
--- a/spec/factories/merge_requests.rb
+++ b/spec/factories/merge_requests.rb
@@ -40,6 +40,10 @@ FactoryGirl.define do
       state :closed
     end
 
+    trait :opened do
+      state :opened
+    end
+
     trait :reopened do
       state :reopened
     end
diff --git a/spec/services/delete_merged_branches_service_spec.rb b/spec/services/delete_merged_branches_service_spec.rb
index a41a421fa6e..7b921f606f8 100644
--- a/spec/services/delete_merged_branches_service_spec.rb
+++ b/spec/services/delete_merged_branches_service_spec.rb
@@ -42,6 +42,19 @@ describe DeleteMergedBranchesService, services: true do
         expect { described_class.new(project, user).execute }.to raise_error(Gitlab::Access::AccessDeniedError)
       end
     end
+
+    context 'open merge requests' do
+      it 'does not delete branches from open merge requests' do
+        fork_link = create(:forked_project_link, forked_from_project: project)
+        create(:merge_request, :reopened, source_project: project, target_project: project, source_branch: 'branch-merged', target_branch: 'master')
+        create(:merge_request, :opened, source_project: fork_link.forked_to_project, target_project: project, target_branch: 'improve/awesome', source_branch: 'master')
+
+        service.execute
+
+        expect(project.repository.branch_names).to include('branch-merged')
+        expect(project.repository.branch_names).to include('improve/awesome')
+      end
+    end
   end
 
   context '#async_execute' do