"I was totally shocked because it's such a small space – everyone went crazy!" said Kyle Luker, who shot the video of the award-winning Grammy singer playing "Shake It Off".
He had been at the club for about 90 minutes when Swift came on stage.
Actor Jesse Tyler Ferguson will host the event and will join Swift on stage to dance and sing.
The star of "Modern Family" thanked Swift on Twitter.
"I'm so glad I did not have to keep this secret – see who came to celebrate Stonewall's 50th Anniversary at Stonewall Inn. @ Taylorswift13, you're a jewel Thank you for everything you do for the LGBTQ community. emoji heart) you! "he wrote, ending the tweet with a rainbow emoji
Friday was a busy day for Swift.
She has also released a new single from her next album, "Lover", due out on August 23rd.
A video for the song "You must calm down" falls on Monday.
The lyrics of the song defy bullies on the Internet and express their support for the LGBTQ community.