At the end of next season, Bayern then have the option to bring him back for the final year of his contract at the Allianz Arena.
"I think this is the best decision for all three parties," said Bayern chairman Karl-Heinz Rummenigge.
"Jan will certainly get the match practice at Schalke that he has not been able to get so far in Munich."
Kirchhoff has appeared only 11 times for Bayern since joining them from Mainz in the summer, and his move to Schalke should enable him to play more frequently again in the top flight.
"We're delighted that we've been able to complete this loan deal because I'm convinced that Jan can help us further," said Schalke's director of sport Horst Heldt.
"He can play both in the centre of the defence and in the defensive midfield. Jan's strengths are in the air, his passing and his tackling."
The Germany Under-21 international has found it hard to break into a Bayern defence boasting Dante, Jerome Boateng and Daniel van Buyten, while Javi Martinez has also been picked ahead of him by coach Pep Guardiola at the heart of the defence.