Nakagami made his MotoGP debut with LCR in 2018 and has remained with the outfit ever since.
His side of the LCR garage, which is backed by Idemitsu, has been set up specifically for a Japanese rider, which has offered him job security.
His position has become a bit more uncertain over the past two seasons as Japanese young gun Ai Ogura, who races in Moto2 currently with Honda Team Asia, has been repeatedly linked to an LCR move.
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Ogura elected to stay in Moto2 for 2023 and will continue in the class next season, after signing a deal to join the new MT Helmets squad – who will step up from Moto3 to take Pons Racing’s grid slots.
Throughout Honda’s miserable 2023, Nakagami has been its most consistent rider, scoring 35 points.
In recent weeks, Nakagami’s future with Honda and LCR looked more assure, with the squad announcing on Tuesday morning that it will continue together for 2024.
"I'm proud to count on Nakagami for another year,” team boss Lucio Cecchinello said.
“He's a fast rider who can get good results, and alongside HRC, we believe it's time to keep pushing, as he's one of the most experienced guys with this bike.
“We will give our best to fight for the positions we aim for.”
Nakagami added: “I feel LCR is part of my family, and of course, I'm excited to be with them for another season.
“I want to thank them and HRC for the opportunity, as I know we are a good match. Now it's time to work even harder to be ready for the future.”
Nakagami will join Zarco at LCR next year, who turned down a one-year extension with Ducati at Pramac to pen a two-year factory contract with Honda.
He will replace Alex Rins, who will join Yamaha in place of Franco Morbidelli – the Italian signing with Ducati for next season to replace Zarco at Pramac.
Most of the grid for 2024 is now in place, with only KTM’s logjam in its bid to find a place for Pedro Acosta, Gresini’s second seat and Marc Marquez’s final decision on his immediate future with Honda to be sorted.