His four bandmates appeared a little lost and confused as they took the stage at the O2 Arena without their fifth group member, and Liam Payne took to the mic explaining he had no idea where Styles was.
Midway through his thank yous, Styles dashed to the platform and announced he had been in the toilet.
He said, "I'm really sorry, I was having a wee! The toilets are miles away!"
His apology prompted Brits host James Corden to poke fun at the pop star as One Direction exited the stage. The comedian quipped, "He couldn't even wait 'til the end of the show."
Corden revisited Styles' embarrassment moments later as he introduced Katy Perry to the stage for the Best British Single presentation and suggested the singer may not have been alone in his toilet stall.
He joked, "My money was on Harry Styles (winning this award), but after what just happened in the toilet..."
In fact Rudimental's 2013 number one Waiting All Night was named the winner.
Corden later came across Styles as he wandered among the audience during the show and added, "I don't care what you were doing in there, as long as you're careful."