Following the Olympics, Murphy competed at the 2012 World Short Course Championships in Istanbul, where he won a gold and bronze medal. His bronze came in the 200-meter backstroke with a time of 1:48.86, finishing behind Radosław Kawęcki and Ryan Lochte. Murphy also earned a gold medal in the 4×100-meter medley relay for his participation in the heats, swimming the backstroke leg with a time of 50.91.