The former Manchester United and England midfielder, who previously had a spell as caretaker boss at Old Trafford, had been in charge at Boro since October 2022.
The 43-year-old guided Middlesbrough to the Championship playoffs in the 2022/23 season, but they have missed out on the top six in the past two campaigns.
"Middlesbrough Football Club has today parted company with head coach Michael Carrick," the club said in a statement.
"Michael's assistants, Jonathan Woodgate and Graeme Carrick, have also departed the club.
"We'd like thank Michael, Jonathan, and Graeme for all their hard work and unwavering commitment. We wish them all the very best for the future."
Middlesbrough won just one of their final six league games to finish 10th in the Championship table, four points off the playoff spots.