In 2016 Niyonsaba won the 800 meters at the 2016 IAAF World Indoor Championships in 2:00.01. Later that year Niyonsaba carried the flag for Burundi at the 2016 Olympic Games in Rio. She concluded her competition with her first Olympic medal, a silver in the women's 800m in a time of 1:56.49, behind Caster Semenya of South Africa.