The 40-year-old ran over the rodent on lap 13 at Circuit Gilles Villeneuve, with the impact tearing a hole in the floor of his SF-25.
Ferrari later confirmed the damage likely cost Hamilton approximately half a second per lap for the remainder of the race.
Hamilton, a vocal animal rights advocate and vegan, finished sixth in a race won by Mercedes driver George Russell.
“It was feeling pretty decent up until then,” Hamilton said.
“And then, I didn’t see it happen, but obviously I heard I hit a groundhog. So that’s devastating. I love animals, and I’m so sad about it. That’s horrible. That’s never happened to me here before. It’s never nice to see that – I just hope it didn’t suffer,” he added.
Groundhogs are common on the Montreal circuit, which is located on a man-made island in the Saint Lawrence River.
Despite efforts in past years to prevent wildlife from straying onto the track, animal encounters remain an occasional hazard at the venue.
Russell secured his first win of the season from pole, with Red Bull’s Max Verstappen taking second place.
Hamilton currently sits sixth in the drivers’ standings as the 2025 F1 season nears its halfway point.