The 23-year-old rider joined the Aprilia satellite team in 2023, when it was known as RNF before being rebaptised Trackhouse this year following an American takeover.
"I am thrilled that Raul will join Trackhouse for the future - he has shown the dedication and commitment necessary to excel at the MotoGP World Championship level," team owner Justin Marks said in a statement.
"We're a new organization and learning every day so having a young, hungry, rider like Raul will be tremendously beneficial as we continue to work with Aprilia building the team."
The Madrid-born Fernandez currently sits 14th in the 2024 championship standings with 46 points.
His teammate for next season remains to be announced as Trackhouse's Portuguese rider Miguel Oliveira is currently without a contract for 2025.
