The BBC confirmed that the 30-year-old is leaving at the end of the current series in June "to explore other avenues".
Jones, who finished third in the last season of Strictly Come Dancing, had always planned to step down after three years, his spokeswoman said.
Since becoming the show's 31st presenter in April 2005, he has been filmed flying with the Red Arrows, fighting as a Samurai warrior in Japan and climbing the four highest mountains in the UK. He was also the first civilian to complete a 30 mile "yomp" with the Royal Marine Commandos.
He said: "It's very sad to be jumping ship, but I will still be on-screen until the end of the series whilst working on other projects. I've loved it, lived it ... and now I feel the time is right to leave it."
BBC Children's controller Richard Deverell said: "Gethin has more than lived up to our very high expectations of Blue Peter presenters with his total commitment, willingness to try anything and limitless good humour."
It was recently reported that he will co-present an entertainment news show on BBC News 24.
> Jones 'soiled himself' during interview