In 2016, Bagnaia started the season with a podium finish at Losail and another podium finish at Jerez, finishing 3rd on both occasions. At his home race in Italy Bagnaia secured another 3rd position beating Niccolò Antonelli by 0.006 seconds. Followed by a crash at Barcelona, Bagnaia secured his first Grand Prix win at the historic Assen circuit in his 59th Moto3 race and it was the first win for Mahindra too. He now had 4 podiums in the first 8 races of the season and found himself fighting for the title. After two average races and a crash at Brno, Bagnaia got his first pole position in the rain-affected Silverstone and finished second behind Brad Binder in a thrilling race. Bagnaia won his second race of the season at Sepang, winning the race comfortably with a big gap after Brad Binder, Joan Mir and Lorenzo Dalla Porta all crashed out in the same corner during the beginning of the race, which was filled with multiple crashes. He finished the season with 145 points to place 4th in the Moto3 Championship with a total of 2 wins and 6 podiums. Bagnaia had an opportunity to finish 2nd in the World Championship behind Brad Binder but was unfortunately taken out in both Phillip Island and Valencia by Gabriel Rodrigo. Rodrigo pushed out Fabio Di Giannantonio in Australia who went down and collected Bagnaia with him. In Valencia Rodrigo made a highside crash on the first lap approaching the last corner, again Bagnaia went down unavoidably.