The Welsh manager, 46, joined the Danish club in September last year having been sacked by Leicester City in November 2024 after just 12 Premier League matches. He signed a three-year contract at the Brondby Stadium and was tasked with lifting the club to a new level and restoring a winning culture.
Cooper's final match was a 1-3 defeat to FC Copenhagen in extra time, a result that cost Brondby their place in Conference League qualification for next season. He finishes with a record of ten wins, six draws and 12 defeats from 28 matches in charge.
Scott McLachlan, vice-chairman of the club's board, confirmed the decision on Brondby's official website.
"With the appointment of Steve, we made a choice that we both believed and hoped could lift the club to a new level. It has done so in several respects, but neither the results nor the performances on the pitch have followed suit. That is why we have chosen to say goodbye to both Steve and Alan today."
Assistant coach Alan Tate has also left his role.
Cooper previously managed Swansea City, Nottingham Forest and Leicester in English football. His most celebrated spell was at Forest, where he led the club to Premier League promotion in 2022 for the first time in 23 years before being sacked in December 2023.
Brondby confirmed simultaneously that Julius Ohnesorge, who has served as technical director since the summer of 2025, has been appointed as the club's new director of football.
The club finished fourth in the Superliga — well short of the ambitions set out when Cooper was appointed.