The Shrimps have taken part in the Football League Trophy 5 times, with the first 4 games, all away, resulting in 4 defeats. In 2000-2001 a visit to Sincil Bank, Lincoln resulted in an unfortunate 3-2 defeat with the Morecambe scorers being Julian Dowe and Steve Walters.

A couple of season later in 2002-2003, Shrewsbury Town ended the Shrimps hopes with a 3-0 victory, in a game that had the visitors taken their chances may have ended with a different result. 12 months later the Shrimps ventured in to Wales to take on Wrexham, but ended up on the wrong end again, suffering a 4-1 defeat with a Wrexham defender being our scorer. In the 2004/2005 season we went out at the first hurdle, 3-0 to Huddersfield Town at the Galpharm Stadium, although the scoreline does not reflect the closeness of the game, with 2 of the goals scored late in the game.

The 2005/2006 season saw a young Morecambe side beat Grimsby on penalties after the game ended 1-1 at Blundell Park. Paul Lloyd put the Shrimps in front before Grimsby equalised but successful penalties from Shaun Gray, Garry Hunter, Danny Carlton and Jonathan Smith put the Shrimps through and gave them their first ever home tie in the competition against Bradford City. However, Morecambe went on to lose that game thanks to an injury time winner from substitute Joe Brown.