Parts of Germany and Belgium were heavily hit by floods over the last fortnight. Over 100 people are still missing, with Germany's official death toll standing at 177, while thousands more have been made homeless.
Two of the worst-hit areas have been North Rhine-Westphalia and Rhineland-Palatinate, while storms have also caused disruption in Bavaria.
In response, Bayern have pledged a minimum aid package of £942,000.
The Bundesliga champions have also arranged to play a friendly against Schalke, who are based in the North Rhine-Westphalia city of Gelsenkirchen.
Schalke were relegated to the second tier last season, though with the date for the charity game at Veltins Arena not yet confirmed, Bayern pledged the financial support immediately.
"The images of the flood disaster shocked us," said Bayern president Herbert Hainer.