The university says Thirsk, who is 60, was unanimously elected by members of the institution's senate.
He is to take over from current chancellor Jim Dinning on July 2.
Thirsk graduated from the university's Schulich (SHOO'-lick) School of Engineering in 1976 with a degree in mechanical engineering.
He holds the Canadian record for the most time spent in space.
The university says Thirsk will play a pivotal role in its "bold journey" towards becoming one of the country's Top 5 post-secondary research schools.
"Robert Thirsk has been a hands-on member of our university community for many years," Dinning said in a release Friday. "Bob's long list of accomplishments, his integrity, and his passion for research and education will inspire students, faculty, staff and alumni for generations."