After playing in the Toffees' pre-season friendlies against Wrexham and Shrewsbury Town, on 6 August 2002 he was signed by then Blackpool manager Steve McMahon, initially on loan for one month at the start of the 2002–03 season.

[13] On 9 December in a Football League Trophy match against Stockport County, Southern collapsed midway through the second half and he needed keyhole surgery on his knee later that month which revealed he had a slight tear in the medial cartilage, which was removed.

[15] When Blackpool won the Football League Trophy at the Millennium Stadium in Cardiff on 21 March, Southern was left out of the squad by Steve McMahon, who chose his son, Stephen, ahead of him.

[21] On 28 April he was named the Professional Footballers' Association (PFA) Player of the Year for League One in an online poll voted for by supporters.

[22] On 21 April 2007, Southern scored an 85th-minute winning goal as Blackpool beat Cheltenham Town 2–1 to guarantee the club a play-off position in League One in the 2006–07 season.

Southern scored Blackpool's winning goal on 11 August 2007 in their first match back in the second tier of English football for 29 years as they beat Leicester City 1–0 at the Walkers Stadium on the opening day of the 2007–08 season.

[26] On 1 December Southern suffered ankle ligament damage in a 1–0 win over Queens Park Rangers at Bloomfield Road, and had an operation later in the month.

[32] He was able to maintain his fitness during his treatment, and two months after his operation he returned to the side, as captain, on 28 January;[33] however, he had to leave the game before the hour mark after suffering a serious gash to his leg.

[35] Southern made his Huddersfield début in the League Cup first round 2–0 away defeat at Preston North End on 13 August 2012 playing the full 90 minutes.

[39] After struggling to make the Fleetwood first team following the loan spell in 2015, Southern left the club by mutual consent early the following year.