The separation ends an 11-year association between Marquez and Honda and clears the way for the Spaniard to ride a Ducati next year.
Marquez's younger brother Alex rides for Ducati's satellite Gresini Racing team and the team have been waiting for Marc to make a decision.
There was no immediate comment from the team on Wednesday.
"Both parties agreed it was in their best interests to each pursue other avenues in the future to best achieve their respective goals and targets," the Honda Racing Corporation statement said.
The Spaniard has struggled with injury and an uncompetitive bike this season, although he finished a season-high third in a rain-hit and shortened Japanese Grand Prix at the weekend.
Before that he had finished only three races with a best finish of seventh at Misano in Italy.
Honda have not been able to match the pace of the Ducati bikes, leading to Marquez attempting to ride his bike beyond its limits and crashing several times.
Marquez joined the Repsol Honda team in 2013 and has won 59 races with them as well as taken 101 podiums and 64 pole positions.
His first victory in the top class was on a Honda in Austin, Texas, in 2013 - making him the youngest MotoGP winner on his way to becoming the youngest champion in the premier category.
However, a crash in the season opener in 2020 saw Marquez require arm surgery which ended his season prematurely, while diplopia (double vision) caused by concussion after a crash caused him to miss races in 2021 and 2022.
His brother Alex impressed with Gresini and has already claimed more than double his points tally from last season after making the switch from LCR Honda.
