The Brazilian was left out of Barca's squad for their opening league game away at Athletic Bilbao tonight, and had been linked with a move away from the Nou Camp all summer.
The former Liverpool midfielder moves to the German side on loan with an option to buy.
A tweet from their official account said: " #FCBayern and @FCBarcelona have agreed a deal in principle for the transfer of @Phil_Coutinho on loan with an option to buy. More to follow..."
A further statement on the Bundesliga side's website stated that the deal is a season long loan with an option for it to be made permanent after that.
Coutinho is expected to arrive in Munich over the next few days to complete a medical and sign a contract for his new side.
Bayern chairman Karl-Heinz Rummenigge said: “The name doesn't matter, only the quality. We've watched him for quite some time."