In January 2014, Thompson made the move to Southend United a permanent one for undisclosed fee, signing an 18-month contract. Just after finishing his loan spell, Thompson attracted interests from two clubs before Southend United won the race to sign Thompson. Thompson's first game after signing for the club on a permanent basis came on 18 January 2014, where he set up a goal for Barry Corr, in a 3–0 win over Chesterfield. Thompson ended his season, making sixteen appearance (as well combining his loan spell at Southend United) after he injured his calf, although he never played throughout the 2013–14 season despite being fit and being once on the bench.
The next season, Thompson missed the first four matches, due being on the bench and made his first appearance, coming on as a substitute in the first half, in a 2–0 loss against Plymouth Argyle on 30 August 2014. Since recovering from a calf injury, Thompson have established himself in the 2014–15 season despite missing out for four matches in late-December. Thompson was once again on the sidelined during a match against Mansfield Town on 3 April 2015 when he was injured in the first half and had to be substituted by Cian Bolger. After having surgery, it was announced that Thompson would be out for the remainder of the season and ended his season, making twenty-nine appearance in all competitions. Despite being absent, the club went on achieve promotion to Football League One after beating Wycombe Wanderers in the play-off final.