The 22-year-old only played once for Chelsea's senior side, and he made his debut in the FA Cup against Derby in 2014.
The midfielder spent the last two seasons on loan at the Eredivisie side Vitesse Arnheim where he helped the club to win the Dutch Cup.
The U21 international, who played four games in the Under-21 European Championship this summer, also had loan spells at Sheffield Wednesday and MK Dons.
His loan period now continues at Middlesbrough, after he signed a new five-year contract for the Blues.
"It's going to be an exciting season. I'm here to give my input and hopefully get the club back to the Premier League", Baker said on Boro's website.