Thousands have crossed into Germany via Hungary and Austria with Munich's train station one of the main points of entry.
The plight of those fleeing conflict in their own countries such as Syria, as well as economic migrants escaping poverty, has polarised opinion in Europe, with the amount of new arrivals stretching the EU's asylum system, as well as straining relations within the bloc.
"FC Bayern see it as its social responsibility to help those fleeing and suffering children, women and men, to support them and accompany them in Germany," Bayern CEO Karl-Heinz Rummenigge said in a statement.
Bayern's youth academy will set up the training camp for kids, in conjunction with the city of Munich and apart from regular training, it will also offer meals and German language classes.
The senior team will be accompanied by migrant children when they enter the pitch for their next home game against Augsburg on Sept. 12 with the club also planning a friendly with one million euros of revenue going towards helping migrants.
"FC Bayern is taking a stand and I am happy about the club's involvement," Munich mayor Dieter Reiter said. "That is why I happily approved the city's support."
Germany expects to receive 800,000 asylum seekers this year, four times more than in 2014, Germany's Labour and Social Affairs Minister Andrea Nahles said on Thursday.
The wave of people arriving in Europe and Germany has sparked an outpouring of sympathy and acts of solidarity in the country from clubs and football fans alike.
Banners with "Refugees welcome" or "Welcome to Germany" were visible in almost every Bundesliga match last week while many teams have also invited migrants to watch their games from the stands.
The German football association (DFB) on Wednesday issued a video message condemning any attacks on migrants or on their accommodation in Germany as well as any form of xenophobia.
A friendly game against a "Refugees United" team next week is also planned with DFB employees.
($1 = 0.8982 euros)
(Reporting by Karolos Grohmann; editing by Toby Davis)
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