In the 2011–12 season, Czisny was assigned to 2011 Skate America and 2011 Trophée Eric Bompard as her Grand Prix events. She won the gold medal at Skate America and bronze at Trophee Bompard. She was first in the free program at Bompard with 121.90 points, setting a new personal best international free skate score. Czisny qualified for the Grand Prix Final. She sustained a calf injury during a practice session on December 8, explaining "it was the way I picked on a flip jump." After team doctors determined that she would not make the injury worse, Czisny went on to compete and finished 5th at the event. She won the silver medal at the 2012 U.S. Championships. After the 2012 Challenge Cup, where she took bronze, she decided not to include the double axel-triple toe combination in her program at Worlds. Falling twice in the short program and five times in the free skate, she placed 22nd overall at the 2012 World Championships.