She received her B.S. in Biology with Highest Honors from Georgia Institute of Technology in 2007. She received her Ph.D. in microbiology and immunobiology from Harvard University in 2013. During her graduate work she studied the pathogenesis of Shigella flexneri, Listeria monocytogenes and Chlamydia trachomatis. Her Ph.D. dissertation investigated how C. trachomatis infection suppresses immune function in mice. From 2013-15, Dr. Fankhauser held the position of Postdoctoral Fellow at the Emory Atlanta campus where she studied the pathogenesis of the bacterium Burkholderia cenocepacia.