Boothroyd led Colchester to seventh in League One this season, having taken charge of the U's in the summer. He previously managed Watford.
"Of course, we have to build slowly and look to improve on previous results and league finishes but you know me well enough by now to know that I am qujite ambitious and I want to be the best that I can be and as a manager," he said.
"I want to keep improving and pushing up the table as that is where everyone wants to be in the promised land."
Gary McAllister, who had been linked with the manager's position at Coventry, has been named first-team coach at Middlesbrough. Jim Blyth joins as goalkeeping coach.
The Reading midfielder Brynjar Gunnarsson has signed a one-year contract extension.
Adam Lockwood, the defender, has signed a two-year contract extension at Doncaster Rovers.