The deal includes a loan fee and contains the option for Fluminense to make the move permanent this summer if certain clauses are met.
Marquinhos has spent the past three weeks playing for Brazil’s Under-23 side at the CONMEBOL Pre-Olympic Tournament, but that is now finished and he is wrapping up his move to Fluminense.
The 20-year-old, who joined Arsenal in the summer of 2022 from Sao Paulo for around £3million, had also been attracting interest from Corinthians.
Marquinhos, however, elected for Fluminense after being won over by the Brazilian’s side head coach, Fernando Diniz.
The loan will be the third of Marquinhos’ Arsenal career after also spending time at Norwich and Nantes.
The winger was at French club Nantes during the first half of this season, but he made just three league appearances and his spell was ended in January.
That sparked interest from sides in Brazil, where the transfer window does not close until the start of March.
Before his loan to Norwich in January last season, Marquinhos made six appearances for Arsenal and scored one goal.