Aru started his 2016 season, at the Volta a la Comunitat Valenciana where he finished 6th overall. He then raced the Volta ao Algarve, and finished 9th overall after taking 2nd place on the last stage. He took his only victory of the season, at the Critérium du Dauphiné where he won Stage 3 after attacking on the downhill inside the last of the stage. His main goal of the season was the Tour de France, and after Stage 8 Aru was 7th overall but dropped to 13th on the following stage to Andorra Arcalis. He managed to get into the top 10 again on Stage 12 to Mont Ventoux. He had a mechanical problem on the stage, and had problems getting back into the bunch before the climb to Mont Ventoux. He received help from the Astana team car, as he was paced for a while, resulting in a time penalty post-stage. On the last mountain stage he was not feeling well, and ended up losing 13 minutes to his main rivals, dropping to 13th place in the general classification.