In the 2012–13 season, Czisny received an assignment to the NHK Trophy but withdrew in order to continue her recovery from surgery. She hoped to compete at the 2013 U.S. Championships. On January 12, 2013, at the 2013 Fox Cities Invitational in Appleton, Wisconsin, Czisny dislocated her left hip when she fell on a triple flip. She was taken to hospital where her hip was moved back into alignment. Her withdrawal from the U.S. Championships was confirmed when she had to undergo another hip surgery on her left hip.