An experienced and solid defender, Barker has now made more than 500 appearances in his career.
The Club captain made 43 appearances last season and was another player to suffer injury woes.
Barker missed three weeks of action before the JPT Final at Wembley but was fit to lead the side out against Crewe Alexandra.
The centre-back scored his first goal for the Club in the second leg of the 2011/12 play off semi-final against Crewe Alexandra, which was also his 100th appearance for Blues.
Barker, whose brother Richie manages at Crawley Town, has also played for Barnsley, Cardiff, Stoke, Colchester, QPR and Plymouth where he worked with former Blues boss Paul Sturrock.
Barker was voted Player of the Year during his first season at Southend and has now been with the Club for three years.