The 23-year-old joined the German and European champion 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."
Schalke general manager Horst Heldt admitted he was thrilled to land a player of Kirchhoff's versatility as Jens Keller's side looks to climb back up the Bundesliga table.
"We are delighted this loan deal was possible and I am convinced that Jan will help us to improve," he said. "He can play as a center back and in defensive midfield. Jan is superb in the air, has a good passing game and is strong in duels."
Kirchhoff began his career with Eintracht Frankfurt before moving to Mainz in 2007.