The 2016 Moto3 season was a part of the 68th F.I.M. Road Racing World Championship season. Danny Kent was the reigning series champion but did not defend his title as he joined the series' intermediate class, Moto2.
The riders' championship title was won by Ajo Motorsport rider Brad Binder, after a second-place finish at the Aragon Grand Prix gave him an unassailable lead over his title rivals with four races remaining. Binder, who finished each of the first seven races on the podium, took the championship lead after the second race in Argentina, and took his first Grand Prix victory at the Spanish Grand Prix – starting from 35th on the grid. With four additional wins prior to Aragon, Binder was never headed in the championship thereafter to become South Africa's third world motorcycle racing champion, after Kork Ballington and Jon Ekerold. Binder took two further victories before the end of the season, in Australia and Valencia, en route to an eventual championship winning margin of 142 points over his next closest competitor. Compared to Binder's seven wins, no other rider was able to take more than two, with eight fellow riders taking at least one win during the 2016 season.
A fourth-place finish in Valencia sealed the runner-up position for Gresini Racing's Enea Bastianini. Despite missing two races through injury and a slow start to the season, Bastianini then achieved six podium finishes in nine races, including his only win of the season in Japan. Five riders were also in position to take third place at the finale; top Mahindra rider Francesco Bagnaia, Jorge Navarro and a trio of rookie riders also battling for Rookie of the Year honours, Nicolò Bulega, Joan Mir and Fabio Di Giannantonio. Bagnaia was taken out of the race by Gabriel Rodrigo, with a ninth-place finish for Navarro allowing him to take third position by five points. Both riders took two victories during the season; Navarro winning in Catalonia and Aragon, with Bagnaia doing so at Assen and Malaysia, the first wins for Mahindra at Grand Prix level. Mir and Di Giannantonio battled on-track in Valencia for the top rookie position, which ultimately went to Mir, as he finished second to Di Giannatonio's fifth position. Mir won the Austrian Grand Prix, one of two rookies to win during 2016.
Four other riders won races during the season; the other rookie winner Khairul Idham Pawi took two wet-weather victories in Argentina and Germany, becoming the first rider from Malaysia to win at World Championship level. Single race wins went to Romano Fenati in Austin, before a mid-season dismissal from Valentino Rossi's team, Niccolò Antonelli won the season-opening race in a photo-finish in Qatar, while John McPhee took his, and Peugeot's, first Grand Prix win in wet conditions at Brno. With nine wins during the campaign, KTM won their fourth Moto3 constructors' title in five years, finishing 32 points clear of Honda, with six wins. All four full-season manufacturers took at least one win.