Jack Saddleback is the first transgender, two-spirit, First Nations person elected to the post.
He says that raising the pink, blue and white transgender pride flag at Convocation Hall on Monday was "very historic and meaningful."
The flag will also be raised Tuesday at the legislature.
Saddleback says for many years, he felt invisible but now he's watching the campus "coming out to ensure that all our community members are respected, included, and accepted."
He says it's important for current and future students to see diversity in leadership and support from campus.
"When I was first thinking about going for the president position it was quite a struggle for me because, I'll be honest, I had never seen myself in that position," he says. "I never saw ... a gay man, a trans man in this type of role before."
University president Gordon Barnhardt announced Monday that two new awards will be handed out, each worth $2,500. The transgender student award and two-spirit student award will be presented in the fall 2015-16 semester.
"The University of Saskatchewan is a place where people are learning new things about themselves, about each other," said Barnhardt. "I think the university is also a place where you should have free speech and free expression. What a place to have a week such as this."