In 2012, she ran the second 10 km leg of a marathon relay at a festival celebrating 50 years of Ugandan independence. After advancing from fifth to second, she spent four hours in a coma.[7]
Nakaayi was the flag bearer for Uganda in the closing ceremony of the 2016 Rio Olympics.[8]
The following month, she became the world 800 m champion in Doha, Qatar, improving her own Ugandan record to 1m 58.04s. She held off Raevyn Rogers, who made a late surge to claim silver in 1:58.18, while Ajeé Wilson finished third in 1:58.84. Nakaayi was joined in the final by compatriot Winnie Nanyondo in fourth.[10]
Nakaayi competed in four 800m events of the World Indoor Tour and improved her Ugandan indoor record three times.[12] Racing in Karlsruhe, Val-de-Reuil, Liévin, and Toruń, she finished in positions 1–1–2–2 respectively, with bests of 1:58.58 (Liévin, lost by 0.12s to Natoya Goule) and 1:59.55 set in France.[4][13] She placed second in Toruń in a triple blanket finish with her time of 2:00.19 equalled by Ethiopia's 19-year-old Tigist Girma, and both behind Catriona Bisset who was 0.03 seconds quicker (photo finish).[14] In March, Nakaayi won the bronze medal at the World Indoor Championships held in Belgrade in a time of 2:00.66, behind Wilson (1:59.09) and Ethiopia's Freweyni Hailu (2:00.54), who overtook Nakaayi just before the finish line.[15] She won comfortably, however, with both Goule (4th) and Bisset (5th).[16]