Omeruo made 14 appearances for Boro on loan last season and boss Aitor Karanka was keen to bring him back to the Riverside Stadium.
The 20-year-old went on to play for his country at this summer's World Cup in Brazil, where he featured in all four of their games.
“He is a very important player to us,” Karanka told the club's website.
“He’s someone I love to have with us because he’s a player who came here from Chelsea and his mood was always perfect.
“He was always happy and fighting for his position.
“He was handed the opportunity to play in the World Cup and he is now coming back to us a better player.”