Malik, 22, has been in the headlines recently after he left their tour midway to be with his fiancee Little Mix singer Perrie Edwards amid rumours of cheating.
The allegations started after a photo revealed Malik holding another woman around the waist.
In a statement, Malik said he felt it was the right time to make the move.
"I am leaving because I want to be a normal 22-year-old who is able to relax and have some private time out of the spotlight," he said in a statement released by One Direction on social media.
More From This Section
The band's remaining members are Niall Horan, Liam Payne, Harry Styles and Louis Tomlinson. They will record their fifth album this year.
"We're really sad to see Zayn go, but we totally respect his decision and send him all our love for the future. The past five years have been beyond amazing - we've gone through so much together, so we will always be friends.
Simon Cowell, who discovered the boyband on talent show The X Factor, said: "I would like to say thank you to Zayn for everything he has done for One Direction.