The 23-year-old moved to the Allianz Arena on a free transfer from Mainz in the close-season, having agreed a pre-contract deal in January, but has been limited to seven substitute appearances in the league in 2013-14.
Kirchhoff will switch to the Veltins Arena until June 2015, with Bayern and Schalke agreeing a return option at the end of the deal.
Karl-Heinz Rummenigge, Bayern chairman, said in a statement on the club's official website: "Jan will surely get at Schalke match practice, which in Munich so far was not possible.
"We wish him all the best and hope that he will be well developed, so that he, if necessary in 2015, returns to Bayern."
Schalke's sport and communications director Horst Heldt added on their website: "We are very pleased that this loan deal was possible, because I am convinced that we can help Jan.
"He can be used in central defence as well as a defensive midfielder."
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