Flyer majored in geological sciences at Northwestern University, graduating with a bachelor's degree there in 1993. She went to the University of Michigan for graduate study in atmospheric and space science, and completed her Ph.D. in 1999. Her dissertation was The Effect of Upper Level Features in The Atmosphere on Linear Theory and Linearized Benjamin-Davis-Ono Theory for Internal Gravity Waves.[4]
She was a postdoctoral researcher at the National Center for Atmospheric Research from 1999 to 2000, and continued her postdoctoral study with the support of an NSF Postdoctoral Fellowship in the Department of Applied Mathematics at the University of Colorado at Boulder from 2000 to 2003. In 2003, she returned to the National Center for Atmospheric Research with a permanent appointment as a scientist.[4]