I'm a little confused. Do you mean junior ROTC offered at your high school? If it is available, why wait to sign up? I don't think there are minimum fitness requirements to join.
If you are talking about college ROTC, anyone can join and take the leadership and fitness components that are offered.
If you are talking about applying for a national ROTC scholarship, then yes, that process begins at end of junior year or early senior year. And, yes, again, you need to pass a physical fitness test as part of the application process. There are several application cycles for each of the various service branch's ROTC scholarships, and they are all different, so you'll have to check the deadlines of the one(s) you're interested in. Your fitness test must be taken well before the document submission deadline for the cycle in which you're applying, in order to allow time for the scorer to process and submit the results. If this is your plan, you have plenty of time to be ready physically. There are many online training programs you can find, or you might consult a trainer or your PE teacher for advice on getting into shape.