Wagner began the 2011–12 season at the 2011 Skate Canada International. She placed second in the short program and third in the freeskate to win the bronze medal overall. At the 2011 NHK Trophy, Wagner placed fifth in the short program and third in the freeskate to finish 4th overall. At the 2012 U.S. Nationals, she ranked third in the short program. She was first in the free program and won her first national title.