The sentence, handed down in Vancouver provincial court, means he will have a criminal record.
Rupert, who was 56 when he was arrested and charged with one count of voyeurism last August, received attention in 2013 for his work on a DNA test to catch doping athletes.
His research was funded by the World Anti-Doping Agency. But he lost his position at the university six days after he was charged for secretly watching participants in a study change out of their clothes.
The study involved fitness, meaning participants had to change into fitness clothes to take part.