Java EE is an Enterprise environment based on the Java language. Javascript is a language originally developed for use in web browsers. Javascript and Java are not the same language. Not even close. They share no history. All they have in common is the first four letters of there name. You can use Javascript as part of the web ui for a Java EE application, but in that case the Javascript files are just payload to the Java EE application, on a par with a plain HTML file. They get sent to the user's browser, which is where the Javascript would execute.

If you really only want to learn the one language and don't need the Enterprise features of Java EE then consider Node.js, which uses Javascript on both the server and the client. I've not used that myself, however.

They have nothing in common except the name Java. J2EE is the enterprise edition of Java and JavaScript is a web-based programming language without typing etc. There are a lot of differences between them and they serve very different purposes. If you want to get into web development learn JS, if you want to get into e.g. android development go for Java.