Czisny finished third at the 2008 Skate Canada International in the 2008–09 Grand Prix series behind Joannie Rochette and Fumie Suguri. At the 2009 U.S. Championships, she won the short program by over five points. She finished third in the long program but won the gold medal due to her lead from the short. Czisny won her first national title, ahead of Rachael Flatt and Caroline Zhang. She earned her second trip to the Four Continents and the World Championships, in which she finished ninth and eleventh, respectively.