diff --git a/lib/internal/test_runner/harness.js b/lib/internal/test_runner/harness.js
index de0cf82682af31..9f78319bef5727 100644
--- a/lib/internal/test_runner/harness.js
+++ b/lib/internal/test_runner/harness.js
@@ -17,8 +17,6 @@ const {
   },
 } = require('internal/errors');
 const { exitCodes: { kGenericUserError } } = internalBinding('errors');
-
-const { kEmptyObject } = require('internal/util');
 const { kCancelledByParent, Test, Suite } = require('internal/test_runner/test');
 const {
   parseCommandLine,
@@ -34,8 +32,7 @@ let globalRoot;
 
 testResources.set(reporterScope.asyncId(), reporterScope);
 
-function createTestTree(options = kEmptyObject) {
-  const globalOptions = parseCommandLine();
+function createTestTree(rootTestOptions, globalOptions) {
   const harness = {
     __proto__: null,
     allowTestsToRun: false,
@@ -65,7 +62,7 @@ function createTestTree(options = kEmptyObject) {
   harness.resetCounters();
   globalRoot = new Test({
     __proto__: null,
-    ...options,
+    ...rootTestOptions,
     harness,
     name: '<root>',
   });
@@ -230,7 +227,11 @@ function lazyBootstrapRoot() {
   if (!globalRoot) {
     // This is where the test runner is bootstrapped when node:test is used
     // without the --test flag or the run() API.
-    createTestTree({ __proto__: null, entryFile: process.argv?.[1] });
+    const rootTestOptions = {
+      __proto__: null,
+      entryFile: process.argv?.[1],
+    };
+    createTestTree(rootTestOptions, parseCommandLine());
     globalRoot.reporter.on('test:fail', (data) => {
       if (data.todo === undefined || data.todo === false) {
         process.exitCode = kGenericUserError;
diff --git a/lib/internal/test_runner/runner.js b/lib/internal/test_runner/runner.js
index e462372a5bd4ed..59263bfada2b12 100644
--- a/lib/internal/test_runner/runner.js
+++ b/lib/internal/test_runner/runner.js
@@ -69,6 +69,7 @@ const {
   convertStringToRegExp,
   countCompletedTest,
   kDefaultPattern,
+  parseCommandLine,
 } = require('internal/test_runner/utils');
 const { Glob } = require('internal/fs/glob');
 const { once } = require('events');
@@ -566,7 +567,14 @@ function run(options = kEmptyObject) {
     });
   }
 
-  const root = createTestTree({ __proto__: null, concurrency, timeout, signal });
+  const rootTestOptions = { __proto__: null, concurrency, timeout, signal };
+  const globalOptions = {
+    __proto__: null,
+    // parseCommandLine() should not be used here. However, The existing run()
+    // behavior has relied on it, so removing it must be done in a semver major.
+    ...parseCommandLine(),
+  };
+  const root = createTestTree(rootTestOptions, globalOptions);
 
   if (process.env.NODE_TEST_CONTEXT !== undefined) {
     process.emitWarning('node:test run() is being called recursively within a test file. skipping running files.');