He then played for Hyde United, who loaned him to Fleetwood in August 2004 after he had recovered from an injury to a cruciate ligament of the knne.
[7] In 2008, he was voted as the Premier Division Player of the Year and was presented with the Peter Swales Memorial Trophy after Fleetwood's match against Bradford Park Avenue F.C.
Milligan's time at Southport wasn't too long, he joined Stockport towards the end of the 2013–14 season playing in most of the club's games.
[12] In February 2008 Milligan teamed up with Gavin McCann, then a Premiership player, to launch the first football academy on the Fylde coast.
The Milligan-McCann Academy is aimed at 8- to 12-year-olds and runs at King Edward VII and Queen Mary School in Lytham St Annes.
[13] In October 2008 the academy received major sponsorship from Northern Care to continue coaching sessions at King Edward VII and Queen Mary School each weekend and to run week-long summer courses.