Aitor Karanka, pictured third left
The Spaniard was not involved with Middlesbrough's first-team before and during the 2-0 defeat by Charlton on Sunday with assistant Steve Agnew taking charge as they dropped seven points adrift of Sky Bet Championship leaders Burnley.
Sky sources reported on Saturday that Karanka had stormed out of the club's Rockliffe training ground on Friday and told players he no longer wanted to be their manager.
But an update on Monday morning hinted that Karanka and the club were keen to address the situation positively, rather than part ways.
The 42-year-old is reported to have questioned the team's desire to reach the Premier League following a 1-0 defeat to relegation-threatened Rotherham on Tuesday.
Karanka was reported to have previously fallen out with Boro players Albert Adomah and Stewart Downing after disagreements earlier in the season.
Middlesbrough's two sentence statement on Monday evening read: "Middlesbrough Football Club can confirm that Head Coach Aitor Karanka will be resuming first team duties with the club with immediate effect.
"We have 10 games left this season and as a club we are fully focused on what remains of our Championship campaign."