She claimed her third medal of the season, finishing as the runner-up at an event in St. Moritz, Switzerland on Friday.
European champion Janine Flock of Austria took the gold. Laura Deas of Great Britain was third.
Vathje won gold at her home race in Calgary and grabbed silver in Lake Placid, N.Y., earlier this season.
The 20-year-old Vathje currently sits seventh in the overall rankings.
In the men's event at St. Moritz, Latvia's Martins Dukurs extended his lead in the World Cup standings. Dukurs won the event by 0.60 seconds over Yun Sungbin of South Korea.