Born in Chiba (Japan) on February 9, 1992, Nakagami joined the Japanese Road Race Championship in the GP125 category in 2005 and in 2006 became the youngest ever winner of the Japanese 125cc Championship. The same year he also joined the MotoGP Academy which gave him the chance to compete overseas for the first time in the CEV (Spanish) 125GP series.

In 2007 he decided to focus on the CEV 125GP championship (under the Academy banner) and had the chance to compete as a wildcard in 125cc World Championship at the final round in Valencia. He impressed enough to secure a full-time ride in the 125cc World Championship in 2008, joining the Italian I.C. Team riding an Aprilia and he continued in the Championship in 2009 with Ongetta I.S.P.A. Aprilia.

Despite having offers to remain in the 125cc championship in 2010, Nakagami decided to return to Japan and re-join the Harc-Pro team (with Honda) for 2 years winning the Japanese Moto2™ title in 2011 and was drafted in by the Italtrans Team at the Japan GP as a substitute rider.

The team offered him a fulltime seat for 2012, and in 2013 just missed out on a maiden race victory on numerous occasions – not least when he scored four consecutive second place finishes in the middle of the season. He switched to Idemitsu Honda Team Asia in 2014, but he had to wait until the following year to return to the podium with third in Misano. He remained with the team in 2016 and took his first win in Assen at the Dutch GP, and by the end of 2017 had garnered eight podiums and two poles. In 2018 Nakagami graduated to the premier class to ride with LCR Honda IDEMITSU and was the best qualifying rookie with several appearances in Q2. Nakagami got his best result at the last round in Valencia crossing the line in 6th position (Best Independent Rider of the Spanish round) and was impressive in winter testing. In 2020 he took his first pole position and front row starts as a podium-contender for much of the season. He stays with LCR Honda IDEMITSU in 2021 alongside new team mate Alex Marquez.