Witnesses saw the 29-year-old woman fire at least four shots on Saturday night from the roof of a two-story building, police said in a statement, adding that no players were injured.
A police spokesman said part of the street in the town of Newmarket, north of Toronto, had possibly been marked in the augmented reality game as a "gym," where players gather to challenge each other.
Pokemon fans accidentally wander over US-Canada border
It is not immediately clear how many Pokemon GO players were on the street that night, though the police spokesman said the area has attracted them by the dozens.
"There's nothing to suggest mental health issues," he said.
Police said the woman was arrested without incident and charged with assault with a weapon and possession of a weapon for a dangerous purpose. Each of the charges carries a maximum penalty of 10 years in prison.
Here's how you can play Pokemon Go in Pakistan
Pokemon GO has been an unexpected success from Spain to Australia, doubling the value of Nintendo Co Ltd since the game's launch in the United States earlier this month.
Using mobile devices, players search for virtual Pokemon characters that appear to pop up at office spaces, restaurants, museums and other places. Players score points in various ways, including capturing the Pokemon characters with a flick of a finger on their phone screen.
10 hilarious reactions to Pokémon Go every Pakistani can relate to
The game was also to blame for a rash of car accidents and a slew of mishaps stemming from distracted players.
York Regional Police, which oversees Newmarket, said officers have received "a number of" calls from concerned citizens about people playing Pokemon GO, and while there's nothing illegal about partaking in the game, players should be careful not to trespass.
Last week, two youths in Canada unaware of their surroundings when they were playing Pokemon GO made an illegal border crossing into the United States.
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