Have a Goal
Before you even pick up the phone, it's probably a good idea to have some idea of what you want to talk about. Don't make it too detailed or write out a script of everything you should say; that'll just make you sound awkward. And what if she changes the subject? Then you're scrambling for your lines and everybody's confused.
But having a goal for the conversation is good. It can be a little goal, like talking about the chemistry lab write-up you both have due next week. Or it can be a big goal, like asking her to the homecoming dance. Just make sure you limit it to a couple of mental bullet points so you don't forget why you called halfway through the conversation.