In 1995, El-Khadra joined the faculty at the University of Illinois at Urbana–Champaign, where she was promoted to professor in 2008. Her research makes use of quantum chromodynamics to understand processes in flavor physics. She spent 1998 as a Fellow at the Center for Advanced Study, where she developed and tested new lattice actions. El-Khadra directs the Fermilab Lattice collaboration, and was named a distinguished scholar at Fermilab in 2016.