Kightly made 88 appearances for Burnley after joining from Stoke in September 2013, but ended last season on loan at Championship side Burton Albion.
The 31-year-old played for Southend between 2003 and 2005, featuring in 19 games for the League One club.
He is the Shrimpers' second signing this summer, following the arrival of left-back Stephen Hendrie.
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Southend United have re-signed winger Michael Kightly on a three-year deal following his release by Burnley.