Among the awards and honours Nathan received were the renamed of Singapore University of Social Sciences (SUSS) School of Human Development and Social Services to S R Nathan School of Human Development (NSHD) in 2018, "Bintang Bakti Masyarakat" (Public Service Star) in 1964, the "Pingat Pentadbiran Awam" (Perak) (Public Administration Medal, Silver) in 1967, the "Pingat Pentadbiran Awam" (Meritorious Service Medal) in 1975, and the "Darjah Utama Temasek" (Order of Temasek) (First Class) in 2013; and honorary degrees from the National University of Singapore and SMU.