If you want to echo it out for later execution it's ok
If you want to execute the JS and use the results in PHP use V8JS
V8Js::registerExtension('say_hi', 'print("hey from extension! "); var said_hi=true;', array(), true);
$v8 = new V8Js();
$v8->executeString('print("hello from regular code!")', 'test.php');
$v8->executeString('if (said_hi) { print(" extension already said hi"); }');
You can refer here for further reference: What are Extensions in php v8js?
If you want to execute HTML&JS and use the output in PHP http://htmlunit.sourceforge.net/ is your solution