I started transitioning during my third year at uni. I came out in the summer and started taking testosterone two weeks into the beginning of Fall semester. Interestingly, school is the only place I don't worry about being transgender. I have Title IX (US law) to protect me, and I know if any professor gives me a hard time, they will likely lose their job. The uni has my birthname, since I haven't changed my name yet, but the school has a program where you can put a preferred name that will show up everywhere that matters, like rosters. I still email my profs before class starts to make sure they have the right name, just in case. I have received not even a weird look from my classmates or my professors, and I do not pass AT ALL. I look and act and talk like a girly female, especially at the beginning of the semester, and no one had any issues calling me "Jack" and "he", because that's who I am.
You should also remember that people around our age are the most likely to be accepting of LGBTQ issues, and professors tend to be liberal (read: more accepting). You should also connect to whatever LGBTQ organizations your school has, as they can be great resources if you do run into any trouble. I think you may be surprised about how accepting colleges are. Every transguy I've met at school so far (yes, there are others, three that I've met) gets his injections at the student health center, from the school nurse. ie: THE SCHOOL IS PAYING FOR THEIR TRANSITION and the guys have nothing but great things to say about how easy it is to get the prescription and how understanding the staff is.
I hope it goes well for you. School should not be a place where you are afraid to be yourself.