The Nigeria international, who played in all four of his country's World Cup games, played 14 times for the Championship side last term and will spend the new season with the club.
The Nigeria international, who played in all four of his country's games at the World Cup, spent the second half of last season at the Riverside Stadium.
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Omeruo made 14 appearances in that spell and will hope to make more of an impact after returning to Aitor Karanka's side.
"He is a very important player to us," Karanka told the club's official 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."