diff --git a/.nycrc b/.nycrc
index f5da62b6c3..4ada3bab1b 100644
--- a/.nycrc
+++ b/.nycrc
@@ -17,6 +17,7 @@
     "package-lock.json",
     "**/package-lock.json",
     "node_modules/**",
-    "scripts/**"
+    "scripts/**",
+    "!test/integration/fixtures/stack-trace.fixture.js"
   ]
 }
diff --git a/package.json b/package.json
index ecaffc45cc..e1bdfa85d5 100644
--- a/package.json
+++ b/package.json
@@ -65,8 +65,8 @@
     "test-browser": "run-s clean build test-browser:*",
     "test-coverage-clean": "rimraf .nyc_output coverage",
     "test-coverage-generate": "nyc report --reporter=lcov --reporter=text",
-    "test-node-run-only": "nyc --no-clean --reporter=json node bin/mocha.js --no-forbid-only",
-    "test-node-run": "nyc --no-clean --reporter=json node bin/mocha.js --forbid-only",
+    "test-node-run-only": "cross-env NODE_OPTIONS=--enable-source-maps nyc --no-clean --reporter=json node bin/mocha.js --no-forbid-only",
+    "test-node-run": "cross-env NODE_OPTIONS=--enable-source-maps nyc --no-clean --reporter=json node bin/mocha.js --forbid-only",
     "test-node:integration": "run-s clean build && npm run -s test-node-run -- --parallel --timeout 10000 --slow 3750 \"test/integration/**/*.spec.js\"",
     "test-node:integration:watch": "run-s clean build && npm run -s test-node-run -- --parallel --timeout 10000 --slow 3750 \"test/integration/options/watch.spec.js\"",
     "test-node:interfaces:bdd": "npm run -s test-node-run -- --ui bdd test/interfaces/bdd.spec",
diff --git a/test/integration/fixtures/stack-trace.fixture.js b/test/integration/fixtures/stack-trace.fixture.js
new file mode 100644
index 0000000000..f81f9653a7
--- /dev/null
+++ b/test/integration/fixtures/stack-trace.fixture.js
@@ -0,0 +1,9 @@
+'use strict';
+
+var assert = require('assert');
+
+describe('a suite', function() {
+  it('should succeed', function() {
+    assert(false);
+  });
+});
diff --git a/test/integration/repo-tooling.spec.js b/test/integration/repo-tooling.spec.js
new file mode 100644
index 0000000000..f85adf24b5
--- /dev/null
+++ b/test/integration/repo-tooling.spec.js
@@ -0,0 +1,16 @@
+"use strict";
+
+const { runMochaJSONAsync } = require("./helpers");
+
+describe("repo tooling", function () {
+  it("issue-5663: line numbers are wrong in stack traces when running mocha self tests", async function () {
+    const output = await runMochaJSONAsync("stack-trace.fixture.js");
+    expect(
+      output.failures[0].err.stack,
+      "to contain",
+      // this file needs to be un-excluded from nyc instrumentation, or else this test would fail to catch any
+      // issues with nyc instrumentation affecting stack traces.
+      "stack-trace.fixture.js:7",
+    );
+  });
+});