In addition, the club said it will donate one million euros ($1.1 million) from a friendly match to what it describes as "refugee support projects."
Thursday's announcement comes after a series of fatal tragedies involving migrants and refugees seeking new lives and safety in Europe.
Last week, 71 people were found dead in a refrigerated truck on an Austrian highway; yesterday, the image of a dead Syrian toddler, washed up on a Turkish beach after a failed attempt to reach the Greek island of Kos, shocked the world.
In August, Germany's Federal Ministry of the Interior announced it expected "up to 800,000 asylum applicants and refugees," to arrive in the country this year, a fourfold increase compared to 2014.
"We at FC Bayern consider it our socio-political responsibility to help displaced and needy children, women and men, supporting and assisting them in Germany," Karl-Heinz Rummenigge, the club's chairman said in a release.
Bayern's actions represent the latest gesture of solidarity from German soccer clubs towards refugees, with fans around the country displaying banners with the message, "Refugees Welcome."
At Bayern's next game on 12th September against German rival FC Augsburg, players will be escorted on to the pitch by one German child and one refugee child, "as a mark of support for the integration of refugees," the club added.
Commenting on the club's actions, Mayor of Munich, Dieter Reiter, said, "FC Bayern is laying down an important marker and I am delighted with the club's significant commitment. I have consequently also gladly pledged the support of the city of Munich."