diff --git a/.github/workflows/untrustedPR.yml b/.github/workflows/untrustedPR.yml
index 35c5b9ea4d..d68c414569 100644
--- a/.github/workflows/untrustedPR.yml
+++ b/.github/workflows/untrustedPR.yml
@@ -33,7 +33,15 @@ jobs:
           synthetic_merge_commit=$(git rev-parse HEAD)
           target_branch_commit=$(git rev-parse HEAD^1)
           incoming_branch_commit=$(git rev-parse HEAD^2)
-          merge_base=$(git merge-base "$target_branch_commit" "$incoming_branch_commit")
+          merge_base=$(git merge-base "$target_branch_commit" "$incoming_branch_commit" || true)
+          if [ -z "$merge_base" ]; then
+            # The two tips can exist in a shallow repository without enough
+            # ancestry to discover their merge-base.
+            if [ "$(git rev-parse --is-shallow-repository)" = "true" ]; then
+              git fetch --no-tags --unshallow origin
+            fi
+            merge_base=$(git merge-base "$target_branch_commit" "$incoming_branch_commit")
+          fi
 
           git diff --name-status --merge-base HEAD^ HEAD --diff-filter=MAR -- '*portfile.cmake' | sed 's/[MAR]\t*//' > .github-pr.changed-portfiles
           if [ -s .github-pr.changed-portfiles ]; then (grep -n -H -E '(vcpkg_apply_patches|vcpkg_build_msbuild|vcpkg_extract_source_archive_ex)' $(cat .github-pr.changed-portfiles) || true) > .github-pr.deprecated-function; else touch .github-pr.deprecated-function; fi