The 57-year-old maestro said he will have been with the orchestra in the German capital for 16 years when he bows out, following 18 years in the same position in the central English city of Birmingham.
"As a Liverpool boy, it is impossible not to think of the Beatles question, 'Will you still need me.., when Im 64?' and I am sure that then it will be time for somebody else to take on the magnificent challenge that is the Berliner Philharmoniker," he said in a statement released by the orchestra.
Rattle acknowledged that it was "not an easy decision" and said he looked forward to another five years at the helm in Berlin.
"I love this orchestra and therefore wanted to tell them my decision as early as possible," he said. "I deeply hope that this will give them enough time to start new plans."
It was not immediately clear who would replace Rattle but veterans such as Israeli Argentine-born conductor Daniel Barenboim and Christian Thielemann of the state orchestra in Dresden were seen as possibilities or, in keeping with Berlin's maverick image, a young break-out talent.
Rattle has been quoted as describing his relationship with the orchestra's musicians as at times "turbulent" but he is extremely popular with Berlin's passionate music lovers and his concerts are routinely sold out.
He arrived in Berlin from Birmingham in 2002 and succeeded the Italian Claudio Abbado.
The philharmonic's general manager, Martin Hoffmann, called Rattle's planned departure "very sad news" for Berlin.
"With his outstanding musicality and creativity he has filled new listeners with enthusiasm for the orchestra every day and has shaped the national and international perception of the Berliner Philharmoniker as a vital cultural ambassador for Berlin," he said.
Philharmonic chairmen Peter Riegelbauer and Stefan Dohr said they regretted the orchestra would no longer be under Rattle's baton after 2018.
"We look forward to many exciting projects which are already in the planning stage," they said in a joint statement.