diff --git a/.github/workflows/mutation-testing.yml b/.github/workflows/mutation-testing.yml
index 9e0987fbd5..2da0c5c5b4 100644
--- a/.github/workflows/mutation-testing.yml
+++ b/.github/workflows/mutation-testing.yml
@@ -36,13 +36,6 @@ jobs:
                   fetch-depth: 0
                   persist-credentials: false
 
-            - name: Fetch pull request base
-              if: github.event_name == 'pull_request'
-              env:
-                  BASE_REPOSITORY_URL: ${{ github.server_url }}/${{ github.repository }}.git
-                  BASE_SHA: ${{ github.event.pull_request.base.sha }}
-              run: git fetch --no-tags "$BASE_REPOSITORY_URL" "$BASE_SHA"
-
             - name: Setup Node.js and pnpm
               if: github.event_name == 'pull_request'
               uses: ./.github/actions/setup-node-pnpm
@@ -56,9 +49,10 @@ jobs:
             - name: Enforce executable-line scope and run advisory mutation testing
               if: github.event_name == 'pull_request'
               env:
-                  BASE_SHA: ${{ github.event.pull_request.base.sha }}
                   HEAD_SHA: ${{ github.sha }}
-              run: node scripts/stryker-diff.mjs ci --base "$BASE_SHA" --head "$HEAD_SHA"
+              run: |
+                  BASE_SHA="$(git rev-parse "$HEAD_SHA^1")"
+                  node scripts/stryker-diff.mjs ci --base "$BASE_SHA" --head "$HEAD_SHA"
 
             - name: Upload mutation reports
               id: mutation_report
diff --git a/scripts/stryker-diff.test.mjs b/scripts/stryker-diff.test.mjs
index 403cf62d89..deaba510a9 100644
--- a/scripts/stryker-diff.test.mjs
+++ b/scripts/stryker-diff.test.mjs
@@ -57,6 +57,8 @@ describe("mutation testing workflow", () => {
 		assert.ok(!workflow.includes("ref: ${{ github.event.pull_request.head.sha }}"))
 		assert.ok(workflow.includes("HEAD_SHA: ${{ github.sha }}"))
 		assert.ok(!workflow.includes("HEAD_SHA: ${{ github.event.pull_request.head.sha }}"))
+		assert.ok(workflow.includes('BASE_SHA="$(git rev-parse "$HEAD_SHA^1")"'))
+		assert.ok(!workflow.includes("github.event.pull_request.base.sha"))
 		assert.ok(workflow.includes("steps.mutation_report.outputs.artifact-url"))
 		assert.ok(workflow.includes("open the package's mutation.html file"))
 		assert.ok(workflow.includes("Enforce executable-line scope and run advisory mutation testing"))
@@ -444,6 +446,49 @@ describe("selectFromGit", () => {
 			fs.rmSync(repo, { recursive: true, force: true })
 		}
 	})
+
+	it("does not charge intervening base-branch changes to the pull request", () => {
+		const repo = fs.mkdtempSync(path.join(os.tmpdir(), "stryker-stale-base-"))
+		const runGit = (...args) => execFileSync("git", args, { cwd: repo, encoding: "utf8" }).trim()
+
+		try {
+			runGit("init", "--initial-branch=main")
+			runGit("config", "user.name", "Mutation Test")
+			runGit("config", "user.email", "mutation@example.com")
+			fs.mkdirSync(path.join(repo, "packages/core/src"), { recursive: true })
+			fs.writeFileSync(path.join(repo, "packages/core/src/pr.ts"), "export const pr = false\n")
+			fs.writeFileSync(path.join(repo, "packages/core/src/base.ts"), "export const base = false\n")
+			runGit("add", ".")
+			runGit("commit", "-m", "initial")
+			const staleBaseSha = runGit("rev-parse", "HEAD")
+
+			runGit("checkout", "-b", "feature")
+			fs.writeFileSync(path.join(repo, "packages/core/src/pr.ts"), "export const pr = true\n")
+			runGit("commit", "-am", "change pull request")
+
+			runGit("checkout", "main")
+			fs.writeFileSync(path.join(repo, "packages/core/src/base.ts"), "export const base = true\n")
+			runGit("commit", "-am", "advance base branch")
+			const currentBaseSha = runGit("rev-parse", "HEAD")
+			runGit("merge", "--no-ff", "feature", "-m", "synthetic pull request merge")
+			const mergeSha = runGit("rev-parse", "HEAD")
+			const mergeResultBaseSha = runGit("rev-parse", `${mergeSha}^1`)
+			assert.equal(mergeResultBaseSha, currentBaseSha)
+
+			assert.deepEqual(
+				selectFromGit(repo, staleBaseSha, mergeSha).packages[0].files.map(({ path: filePath }) => filePath),
+				["packages/core/src/base.ts", "packages/core/src/pr.ts"],
+			)
+			assert.deepEqual(
+				selectFromGit(repo, mergeResultBaseSha, mergeSha).packages[0].files.map(
+					({ path: filePath }) => filePath,
+				),
+				["packages/core/src/pr.ts"],
+			)
+		} finally {
+			fs.rmSync(repo, { recursive: true, force: true })
+		}
+	})
 })
 
 describe("mutation exclusions", () => {