In a tweet, Mr Watson said: "After 35 years in full-time politics, I've decided to step down and will be campaigning to overcome the Tory-fuelled public health crisis. I'm as committed to Labour as ever. I will spend this election fighting for brilliant Labour candidates and a better future for our country."
Following his announcement, the Labour Party issued a statement saying: "After 35 years in full-time politics, Tom Watson is stepping down as an MP and Labour's Deputy Leader.
"Labour Leader Jeremy Corbyn has thanked Tom for his contribution to the Party over three decades and paid tribute to the work he has done to take on the vested interests of the Murdoch empire, the big sugar companies and the gambling industry.
"Tom will continue to play an active part in the General Election campaign, as the country faces a stark choice: transformational change for the many with Labour, or more divisive austerity politics serving the few with the Tories.
"After the election, Tom will be focusing on campaigns to overcome the Tory-fuelled public health crisis. He will be setting up a new organisation championing remission for all type 2 diabetics and has a book on 'downsizing' coming out in January about his own health journey."