In the 2006–07 season, Wagner made her Junior Grand Prix debut. She won both the Junior Grand Prix event in Courchevel, France, and the event in The Hague, Netherlands. Her wins qualified her for the Junior Grand Prix Final in Sofia, Bulgaria, where she won the silver medal behind fellow American Caroline Zhang, with a final score of 142.01. At the 2007 U.S. Nationals in Spokane, Washington, Wagner placed third behind Mirai Nagasu and Caroline Zhang, earning herself a spot on the World Junior Championships team. Her bronze medal at the 2007 Nationals was the first time she had placed in the top three at the national championships. At the 2007 Junior Worlds in Oberstdorf, Germany, she landed seven triple jumps in her long program. She finished with the bronze medal behind Zhang and Nagasu, completing the first-ever American sweep of the World Junior podium.