After law school, Waggoner was a law clerk to Justice Richard B. Sanders of the Washington Supreme Court. She then interned with U.S. Representative Linda Smith. In 1998, she entered private practice with the Seattle law firm Ellis, Li & McKinstry (ELM). ELM specializes in constitutional law and many of its clients are religious organizations. According to partner Keith Kemper, it's "perhaps the nation’s largest private law firm made up of Christian attorneys." Waggoner was elevated to partner in 2004.
