The state of changing your gender marker on the birth certificate is currently in flux. In about 4 months, Ontario will have to come up with a new way to regulate it, because the current requirement of "transsexual surgery" was deemed a human rights violation by a court. However, that doesn't help you at the moment.
Passports can currently be changed so that their gender marker doesn't match your birth certificate. You'd need to go to a Service Canada office and ask them for a form to change the gender marker on your passport. They may or may not know what that is, if they don't you'll need to ask for their manager / ask them to look it up. If you are a minor, your parents will probably need to sign the form. You'll also need to go through the whole regular passport application process as well, of course.
This will let you get a 2 year passport (though sometimes they hand out regular 5 year ones, I don't know why) in your correct gender. If you then take your passport to the school folks, they'll probably be willing to match your passport rather than your birth certificate, given they seem supportive. After all, if your passport doesn't need to match the birth certificate, why should their paperwork?
In addition, if you are old enough to get a learner's permit / driver's license, you can get the correct gender marker on that with a letter from a physician saying you are under their care for transitioning. And if you have that and your passport you can get the gender marker on your health card changed as well.
The more IDs in your correct gender the better usually.