Professor Khalili has been awarded various honours, which include Trustee of the City of Jerusalem, an Honorary Degree ofDoctorof Humane Letters from Boston University, and Knight Commander of the Royal Order of Francis I (KCFO).
He also received an honorary Doctorof Laws degree from New York University in 1982, and an honorary Doctorof Humane Letters degree from Yeshiva University in 1986 and from Trinity College in 2005.