The club’s majority owner, Paul Barry, said: “This has been a challenging season which has not gone as any of us would have hoped. There have been lessons for all of us to learn.
“Clearly, Neil left us in a unique set of circumstances last season and we all feel there is unfinished business for him at Cambridge United.
“He made a significant impact at the club over a short period last season. He is a winner and his track record as a head coach speaks for itself.”
Harris, who is Millwall’s all-time top goalscorer and oversaw their promotion to the Championship in 2017, also managed Cardiff and Gillingham prior to his brief stint with the U’s.
At that time, he took over from Bonner, who spent several years on Cambridge’s coaching staff before becoming manager in 2020 and guiding them to the runners-up spot in League Two a year later.
Bonner, whose eight-month spell as Gillingham boss came to an end in January, has been tasked with leading an ongoing review of football operations at Cambridge.
Barry added: “Mark knows the club inside out – its strengths, its culture and values, and also the areas that we must seek to improve.
“He is an exceptional individual and we believe his leadership, strategic thinking and deep understanding of the game can make him an outstanding director of football for us over the long term.”
