diff --git a/lib/platform/github/index.js b/lib/platform/github/index.js
index 4bd81c60a409ea6aae4d227b2338ee03c50c2ee6..c98dac89365ff1cbfbae1c4d0e75c90b975a64f7 100644
--- a/lib/platform/github/index.js
+++ b/lib/platform/github/index.js
@@ -73,6 +73,7 @@ async function initRepo(repoName, token, endpoint) {
     process.env.GITHUB_ENDPOINT = endpoint;
   }
   config.repoName = repoName;
+  delete config.baseCommitSHA;
   config.fileList = null;
   config.prList = null;
   config.prs = {};