At the start of the 2006–07 season, he signed a 12-month extension to his contract. He spent more than two years with League Two side Rochdale, before joining Boston United in the January transfer window of 2007. Boston United were reduced to just 12 professionals on their books in the closing stages of the 2006–07 season, as the club could not afford to pay players wages. Cooksey had not been paid since February, and was spending £30 a day in fuel travelling from his Manchester home. He spent six months at Boston United and played 16 League Two games, but was unable to prevent them from being relegated from The Football League on the final day of the season.