diff --git a/lighthouse-cli/cli-flags.js b/lighthouse-cli/cli-flags.js
index 06e96f93dab2..28f6036424e6 100644
--- a/lighthouse-cli/cli-flags.js
+++ b/lighthouse-cli/cli-flags.js
@@ -11,14 +11,26 @@ const yargs = require('yargs');
 const pkg = require('../package.json');
 const printer = require('./printer');
 
+/**
+ * Remove in Node 11 - [].flatMap
+ * @param {Array<Array<string>>} arr
+ * @return {string[]}
+ */
+function flatten(arr) {
+  /** @type {string[]} */
+  const result = [];
+  return result.concat(...arr);
+}
+
 /**
  * @param {string=} manualArgv
  * @return {LH.CliFlags}
  */
 function getFlags(manualArgv) {
-  // @ts-ignore yargs() is incorrectly typed as not returning itself
+  // @ts-ignore yargs() is incorrectly typed as not accepting a single string.
   const y = manualArgv ? yargs(manualArgv) : yargs;
-  return y.help('help')
+  // Intentionally left as type `any` because @types/yargs doesn't chain correctly.
+  const argv = y.help('help')
       .version(() => pkg.version)
       .showHelpOnFail(false, 'Specify --help for available options')
 
@@ -46,6 +58,9 @@ function getFlags(manualArgv) {
       .example(
           'lighthouse <url> --extra-headers=./path/to/file.json',
           'Path to JSON file of HTTP Header key/value pairs to send in requests')
+      .example(
+          'lighthouse <url> --only-categories=performance,pwa',
+          'Only run specific categories.')
 
       // List of options
       .group(['verbose', 'quiet'], 'Logging:')
@@ -171,6 +186,29 @@ function getFlags(manualArgv) {
           'For more information on Lighthouse, see https://developers.google.com/web/tools/lighthouse/.')
       .wrap(yargs.terminalWidth())
       .argv;
+
+  // Support comma-separated values for some array flags by splitting on any ',' found.
+  /** @type {Array<keyof LH.CliFlags>} */
+  const arrayKeysThatSupportCsv = [
+    'onlyAudits',
+    'onlyCategories',
+    'output',
+    'plugins',
+    'skipAudits',
+  ];
+  arrayKeysThatSupportCsv.forEach(key => {
+    // If a key is defined as an array in yargs, the value (if provided)
+    // will always be a string array. However, we keep argv and input as any,
+    // since assigning back to argv as string[] would be unsound for enums,
+    // for example: output is LH.OutputMode[].
+    const input = argv[key];
+    // Truthy check is necessary. isArray convinces TS that this is an array.
+    if (Array.isArray(input)) {
+      argv[key] = flatten(input.map(value => value.split(',')));
+    }
+  });
+
+  return argv;
 }
 
 module.exports = {
diff --git a/lighthouse-cli/test/cli/cli-flags-test.js b/lighthouse-cli/test/cli/cli-flags-test.js
index 99e676e37551..da55490120d6 100644
--- a/lighthouse-cli/test/cli/cli-flags-test.js
+++ b/lighthouse-cli/test/cli/cli-flags-test.js
@@ -28,4 +28,29 @@ describe('CLI bin', function() {
       assert.ok(optionsWithDescriptions.includes(opt), `cli option '${opt}' has no description`);
     });
   });
+
+  it('array values support csv when appropriate', () => {
+    const flags = getFlags([
+      'http://www.example.com',
+      '--only-categories=performance,seo',
+      '--skipAudits=unused-javascript,redirects',
+      '--skipAudits=bootup-time',
+    ].join(' '));
+    expect(flags.onlyCategories).toEqual(['performance', 'seo']);
+    expect(flags.skipAudits).toEqual(['unused-javascript', 'redirects', 'bootup-time']);
+  });
+
+  it('array values do not support csv when appropriate', () => {
+    const flags = getFlags([
+      'http://www.example.com',
+      '--chrome-flags="--window-size 800,600"',
+      '--chrome-flags="--enabled-features=NetworkService,VirtualTime"',
+      '--blockedUrlPatterns=.*x,y\\.png',
+    ].join(' '));
+    expect(flags.chromeFlags).toEqual([
+      '--window-size 800,600',
+      '--enabled-features=NetworkService,VirtualTime',
+    ]);
+    expect(flags.blockedUrlPatterns).toEqual(['.*x,y\\.png']);
+  });
 });