In October 2018 it was confirmed that Nakagami would remain at LCR Honda on a 2018-spec machine for the 2019 MotoGP season beside teammate Cal Crutchlow. In the first half of the season he regularly achieved top 10 finishes, but a heavy crash at the Dutch TT and a subsequent shoulder injury led to a drop in form. He elected to prematurely end his season after his home Grand Prix to undergo surgery to repair his damaged shoulder and recover before the 2020 season. He was replaced for the final three rounds by KTM-exile Johann Zarco. Nakagami ultimately finished the season in 13th position with 74 points, more than doubling his rookie season.