It has not any meaning. It is just an introduction to a question. In English you move predicate to the beginning: You are a girl. -> Are you a girl? In Polish you just add "czy", so: Jesteś dziewczynką. -> Czy jesteś dziewczynką? :)
By the way, you can skip the word "czy" if you speak in informal language. But then, you must accent that it is the question.
One of the easiest ways I've found to understand this word is to translate it as "whether," or even "if." It's sort of like saying, "Whether you are a girl (or not)?" This will help you in the future, when czy may be followed by more than one option.
Of course, that's not to say you should translate it as "whether." :-) It may help you to use that meaning to parse the sentence in your mind, and then come up with the best (and simplest) translation for it on a case-by-case basis.
If the Polish sentence used "czy", it definitely is a question and thus only "Are you a girl?" can be accepted.
If the Polish question was just "Jesteś dziewczynką?", then "You are a girl?" could be accepted, because it could be someone being surprised that you're a girl.