It happened at about 9.15am on Saturday, May 29 in Mickelgate.
A man suffered a medical episode and crashed his red hatchback car through the window of the pub.
The pub does not open until 12pm so no one was inside.
The man was treated by the ambulance service.
Due to the incident, the pub was closed on Saturday.
In a statement, the owners said: "Due to unforeseen circumstances, we will be closed for today.
"Everyone is okay but until the site clear & safe we will be closed."
City of York Council checked that the building was safe and the bar reopened on Sunday, May 30.
The pub said: "We Are Open.
"A big thank you to the North Yorkshire Police, Fire & Rescue Service. All measures were taken to keep the community safe and resolve the issue as quickly and efficiently."
Full North Yorkshire Police statement:
"The York City Policing team, fire and ambulance service are working together on an incident on Micklegate.
"All measures are being taken to keep the community safe and resolve the issue as quickly and efficiently as possible."
It later updated: "This minor single-vehicle collision was reported by Yorkshire Ambulance at 9.17am who treated a man who had taken ill at the wheel before crashing into the Brewdog pub.
"North Yorkshire Fire made the red hatchback car safe and City of York Council is checking the building and made the area safe."