In the 2009–10 Grand Prix season, Czisny placed fourth at the 2009 Rostelecom Cup and won the silver medal at the 2009 Skate Canada International. Her short program score of 63.52 was the fourth highest of this ISU Grand Prix season, only surpassed by Yuna Kim (two scores) and Joannie Rochette. Czisny placed tenth at the 2010 U.S. Championships; as a result, she did not make the Olympic team and financial support to help cover her mid-five-figure training expenses was cut. She also found out her sister had cancer (in remission as of 2011). Czisny considered retiring but her mentors Brian Boitano and Linda Leaver encouraged her to continue.