The 23-year-old has joined the Gelsenkirchen outfit until the summer of 2015 after struggling for first-team football under Pep Guardiola this season
The 23-year-old joined the German and European champions from Mainz during the summer but has struggled for playing time under Pep Guardiola this season, making just 11 appearances in all competitions to date.
The former Germany youth international has now agreed to move to Gelsenkirchen on an 18-month deal, a move which Bayern CEO Karl-Heinz Rummenigge believes will benefit all parties in the long term.
"I think this is a good decision for all three parties," Rummenigge told the club's official website. "Jan will get definite match practice at Schalke, which wasn't always possible at Bayern.
"We wish him all the best and hope he will develop there, so that, if necessary, he can return to Bayern in 2015."
Kirchhoff, who has operated as both defender and defensive midfielder in his career to date, began his career with Eintracht Frankfurt before moving to Mainz in 2007.