The German international, who was named FIFA's World Goalkeeper of the Year earlier this year, initially joined the club on a five-year contract in 2011.
Bayern's chief executive, Karl-Heinz Rummenigge, told the club's website: "Our goalkeeper Manuel Neuer has today extended his contract until June 30, 2019.
"It's also a mark of his wonderful character, because he's said, 'I want Bayern Munich forever!' I'd like to thank Manuel Neuer very warmly for this."
Neuer has won two Bundesliga titles, the DFB-Pokal, the Champions League, the Super Cup and the Club World Cup since joining the team.