GitHub · Pull requests · Branches · Checked October 26, 2026

GitHub: the branch is not deleted after merging

Deleting a pull request's head branch after the merge is a separate step, done by the "Automatically delete head branches" setting, the "Delete branch" button on the pull request, or a tool calling the API, and the branch's rules apply to it. A ruleset that restricts deletions lets only users with bypass permissions delete the branches whose name matches its pattern, and this rule is selected by default; a protected branch cannot be deleted unless its protection allows deletions (GitHub's available rules for rulesets and about protected branches, checked October 26, 2026).

DELETE /repos/OWNER/REPO/git/refs/heads/BRANCH
204 No Content | 409 Conflict | 422 Validation failed

What keeps a branch

Restrict deletions (rulesets): through the REST API it is the rule type deletion, "Only allow users with bypass permissions to delete matching refs" (GitHub's REST API endpoints for rules). Because it is selected by default, a ruleset made for other rules on a pattern that matches pull request branches keeps those branches too.
A protected branch: by default you cannot delete a protected branch. With "Allow deletions", anyone with at least write permissions to the repository can delete it. A locked branch ("Lock branch") cannot be deleted either.
Automatic deletion: anyone with admin permissions can turn "Automatically delete head branches" on or off, and branch protection rules and repository rules can also prevent branches being deleted automatically. For a pull request from a fork, GitHub uses the fork's setting, and the person merging needs write access to the fork; otherwise the branch is not deleted automatically (GitHub's managing the automatic deletion of branches).
Open pull requests: with write access you can delete branches associated with closed or merged pull requests, but not branches associated with open pull requests; the "Delete branch" button is not shown while there is an open pull request for the branch (GitHub's deleting and restoring branches in a pull request).
Through the API: "Delete a reference" answers 204 when it deletes the branch, 409 for a conflict, and 422 for "Validation failed, an attempt was made to delete the default branch, or the endpoint has been spammed" (GitHub's REST API endpoints for Git references).

After the head branch is deleted

Pull requests based on it: when a head branch is deleted after its pull request was merged, GitHub changes the base branch of the open pull requests in the same repository that were based on it to the merged pull request's base branch (GitHub's merging a pull request).
Restoring it: the head branch of a closed pull request can be restored with "Restore branch" near the bottom of the pull request.

What to do

Find the rule: anyone with read access to a repository can view its active rulesets; look for one whose pattern matches the branch and that restricts deletions. A branch protection rule for the branch keeps it unless "Allow deletions" is on.
Delete it later: someone allowed to bypass the ruleset, or with write access when the protection allows deletions, clicks "Delete branch" on the merged pull request. For a fork's branch, it takes write access to the fork.
The ruleset should not cover these branches: whoever manages the ruleset narrows its pattern, or removes "Restrict deletions" from it.
Another pull request still uses the branch: merge or close that pull request first.

In IntelliJ IDEA: "has been deleted." while the branch is still there

How the GitHub support built into IntelliJ IDEA deletes a merged pull request's branch, in its source (checked October 31, 2026; IntelliJ IDEA: GHPRFileEditorComponentFactory.kt, GHPRDetailsTimelineViewModel.kt, GHPRDeleteMergedHeadAction.kt, GHPRDetailsServiceImpl.kt, deleteRef.graphql, GithubBundle.properties):

Its merge sends only the merge. The IDE deletes the branch only when you ask it to. After the merge, the pull request's timeline shows "Pull Request Successfully Merged" with "You can now delete BRANCH.", and the action Delete Branch ("Delete the merged branch on GitHub") is on.
It offers deletion only while the pull request is merged, GitHub returns viewerCanDeleteHeadRef as true for your account, and the head branch still has an id. Otherwise the same line reads "BRANCH has been deleted." with Restore…, which only opens the pull request in your browser. So that line also appears for a branch that is still there; look at the branch on GitHub, then use the rules above.
It deletes with GitHub's GraphQL API (deleteRef on the head branch), on GitHub only: your local branch is left as it is.
When GitHub refuses, nothing appears on screen: the source writes the error to the IDE's log. The pull request is then loaded again, so the line follows the branch's state on GitHub.

GitHub pull requests in IntelliJ IDEA

Pull Request Inbox for GitHub, a plugin by Lesstep for JetBrains IDEs 2024.1 or later, shows a pull request's reviews, checks and conversations next to the diff, and merges it with the methods the target branch allows. Its merge dialog can delete the pull request's branch after the merge (a branch in the same repository, not a fork's). If GitHub refuses, the notice after merging says the branch was not deleted and names the rules that protect branches from deletion; a refusal answered with 422 too, as the plugin then looks whether the branch is still there. The review inbox, diffs and conversations are free; approving, commenting, resolving and merging are Pro (US$1.50 a month, with a 30-day trial).

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