Thompson followed up her 2015 breakoput season by claiming the rare and coveted sprint double at the Olympic Games in Brazil and became the first woman to do so in 28 years. She clocked winning times of 10.71 seconds and 21.78 seconds for the 100 metres and 200 metres, respectively. Thompson also won a silver in the sprint relay to leave her first Olympic Games with three medals: two gold and one silver.

In a brilliant season Thompson also equalled the national 100 metres record, clocking 10.70 seconds at the National Championships on July 1 to equal the mark set by Shelly-Ann Fraser-Pryce in 2012. Thompson ended the year in glory, winning the diamond for the 100 metres in the IAAF Diamond League by virtue of winning all four of her races and finishing second in the 200 metres Diamond series. She also set a new 200 metres Diamond League record of 21.85 seconds at the Weltklasse meet in Zurich. Thompson was one of three finalist in the voting for the IAAF female athlete of the year, 2016.