Iain Dowie took over team affairs in Brown's absence and, although he was not retained at the end of the season, there has been no way back for Brown.
'I am very sad to be leaving Hull City,' he said. 'My 3½ years at the club were a fantastic experience for me and I am extremely proud of the club's achievements during that time.
'Now that we have reached a resolution, I can now look forward to returning to management in the not too distant future.'
Hull, who are saddled with large debts, are now looking for a new manager to spearhead their attempts to bounce back from the Championship. Paul Hart, the Crystal Palace manager, has been linked with the post.
CPFC2010, the consortium aiming to save Crystal Palace, has moved a step nearer its takeover of the Championship club. According to administrator Brendan Guilfoyle, 'legally binding agreements have been signed which should save the football club', with a final deal set to be completed by the end of July.