The Bavarians, one of the world's richest soccer clubs with a turnover of more than half a billion euros, have not had a home-grown player make a successful transition to the senior team since Thomas Mueller in 2009.
"We have a lot of catching up to do compared to the other big European clubs. That is why we are starting this now," said club president Karl Hopfner during a ceremony on the plot near their Allianz Arena stadium in the north of the city.
"I am convinced that this will become another milestone in Bayern history," he said.
The new facility, to be completed by the start of the 2017/18 season, will have eight football pitches, including one with 2,500-seat stands, a youth academy, offices and a multi-purpose sports hall.
Bayern youth teams are currently using the Saebener street facilities which are home to the club headquarters and the senior team as well.
(Reporting by Karolos Grohmann; editing by Toby Davis)