After scoring twice in Micky Barron`s testimonial game against Leeds in the summer of 2006, Brown found himself in the first team for the beginning of the League Two campaign. It took him a while to establish himself as the team struggled but, after being switched to the right wing by Danny Wilson, he started every game in the second half of the season as Pools surged to promotion. A disappointing season followed for the team in 2007/08 but Brown`s performances were a highlight. He scored 14 goals from the right wing berth and was an overwhelming winner of the players` Player of the Season award. At the start of the next campaign Danny Wilson announced that Brown would be employed as a striker. He began that season in sparkling form and had eight goals to his name when his season was ended in November by his second serious knee injury, this time to his other knee.
Sadly for player and fans alike, injuries would continue to plague Brown for the remainder of his time at Pools. He started only a third of the matches over the course of his last three seasons, scoring just eight times. His time at the club, which had once looked like being a stepping stone to better things, was ended in May 2012 when he was not offered a new contract.