Ghoneim served as annual president of the Endourology Society in 1987. Ghoneim is the recipient of the Egyptian National Scientific Award, 2001, and was a nominee for the European Urology Society annual award in 2004. He was the winner of the SIU-Félix Guyon Medal. Ghoneim was awarded Hamdan Award for honoring distinguished personalities from the Arab World by Hamdan Medical Award in 2014.