Makongoro was educated at Arusha, Bunge and Isike primary schools from 1964 to 1972. He then joined Tabora Boys Secondary School where he obtained his ordinary and advanced level of education. From 1979 to 1990, he served in the army and is a veteran of the Uganda–Tanzania War. Following the Fall of Kampala on 11 April 1979, he was part of the Tanzanian troops that remained there to ensure that law and order prevails.