I have been on hormones for around 7 months, and do not want to cease use of them for any period of time for any reason. However in the case of a Trump presidency I will be fleeing the country as I doubt completely that my rights will be protected under an administration made up of people known for their ties to hate groups and pushing anti-lgbt policies.

I need to know how to continue hormone therapy in Canada as a non citizen, via legal channels(No grey market, no taking birth control pills in an attempt to simulate it, specifically doctor prescribed/ monitored hormone treatment.

I think as long as you have provincial health care you should be good accessing the system. It is not available for visitors though. Citizen, permanent resident, temporary visa holder (student/work) are eligible usually.

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You need to achieve residency, which is province specific.  Sometimes that can be high as 3 month, that you have to prove you live there.  After that you are good.

What you want to avoid is the common workaround of staying six months at a time and then re-entering the States for a day.  While lots of people do it, and it is a legal way to remain in Canada, it means that you are always a visitor, never a resident.  And, in particular, it means no health care coverage. 

It would be legal to see a doctor for prescriptions at your own expense or funded by insurance.

It might be easier to move to a US state that has those types of protections in their state law and constitution.  Though there are of course sane reasons to want to ditch all contact with the US health care payment model...

Seems like an over reaction to flee the country before Trump actually does anything unpleasant; though I'll admit to a certain amount of fear myself about such a thing as well.

That said, take a look at 270towin.com;  no matter what the "nationwide" polls say; the reality is that nationwide polls are completely irrelevant.  We don't do a popular vote for president in the US.  We vote state by state with Electors; and Clinton is absolutely destroying Trump on that map.    Its a Reagan class curb stomping, and I suspect as Trump reveals more of his reckless bravado, he'll lose even more states.   (honestly, there never was much of a chance for any Republican to win this cycle, regardless of who the D or R nominees were.)

It's not so much that I think it's going to happen, as it is wanting to be prepared if it did. That and wanting to leave the country anyways, I'm not fond of the U.S. I'd like to make it out to Toronto, Montreal, or Vancouver eventually.

So with a students visa, I would be able to access hormones through the national healthcare system?
and without a visa I would be able to access hormones by paying out of pocket?

Each province runs its own health care system, so there are differences, and eligibility for foreign students is one area where they differ.  I picked this up with a quick Google search:

QuoteAll international students in Canada must have health insurance. Medical coverage available to international students varies from province to province. In provinces where international students are not covered under provincial health care plans, students must arrange for private health insurance coverage.

You should check the eligibility requirements for the provinces where you wish to study: Ontario, Quebec or British COlumbia.