Witono was born on 10 May 1925 in Yogyakarta. Witono attended "Hollandsch-Inlandsche School" (Dutch schools for native) in Blitar, "Meer Uitgebreid Lager Onderwijs" (More Advanced Primary Education) in Malang, and "Hollandsche Indische Kweekschool" (Substitute Teachers' School) in Muntilan. After attending the "Hollandsche Indische Kweekschool", he initially enrolled at the teacher's school in Blitar in order to become a teacher, but dropped out in 1945 to pursue military career following the independence of Indonesia.