El-Khadra was elected fellow of the American Physical Society in 2011 "for contributions to lattice QCD and flavor physics including pioneering studies of heavy quarks on the lattice, semileptonic and leptonic heavy-light meson decays, the strong coupling constant, and quark masses". She was named to the 2021 class of fellows of the American Association for the Advancement of Science. In 2022 she was awarded a Simons Fellowship.