After graduating from the Vilnius Pedagogical Institute in 1962 Jonas Motiejūnas worked as a physics teacher in a local secondary school. Motiejūnas remained in the education sector throughout his life, eventually becoming a senior research fellow. He was also an accomplished rower, becoming a nine-time champion of Lithuania, with two titles in the eight (1962–63), four titles in the coxless fours (1963–65, 1969), and two in the coxed pairs (1966–67). He also was a two-time Soviet champion with titles in the coxless fours (1965) and the eight (1968). At international competitions Motiejūnas placed fourth in the coxless fours at the 1964 European Championships in Amsterdam, before placing seventh in the same event at the Tokyo Olympics later the same year.