Your EJB would be bound to the JNDI tree by a specific name. You will have to do a lookup using the InitialContext object and pass the jndi name of the bean to the lookup method. The lookup is going to return you a EJB home object or a remote/local interface depending on which version of EJB you are using.
For EJB 2.x, the code would look like:
This is just a pseudo-code. You might have to lookup some examples online or in some books to understand what each of the above statements are meant to do. Note that for EJB3, this is going to be different. Infact, you dont even have to write code to do the lookup. You can rely on Dependency Injection.