Wijayatunga was married to Kalukapuge Karuna Perera (B.A., Dip.
Wijayatunga and Karuna are the parents of three sons (Widyasagara, b. 1965, Chakrapani, b. 1967 and Chandrakeerthi, b. 1970) and a daughter (Shyama Kumari, b. 1969).