The utility man struggled in what now appears to be his final season for the Championship club.
The 24-year-old's existing deal that he signed when he joined the Whites in 2013 is set to expire in the coming weeks, but the Yorkshire Evening Post reports that the former Manchester United man thought that he had agreed an extension last year until the end of next season.
However, the Yorkshire Evening Post claims that while the player signed the deal, the club did not complete the necessary paperwork which has left the extension up in the air.
The news of Wootton's imminent departure is unlikely to be poorly received by supporters. Though the Englishman initially hinted that he could be a rival for either Tom Lees' and Jason Pearce's positions at centre-back when he first arrived, it is safe to say that he has not kicked on during his time with the club.
His versatility saw him used at right-back this season while Sam Byram was not being used in the first-team and Gaetano Berardi and Charlie Taylor were sidelined with injury.
However, his frequent mistakes - including an embarrassing own goal against Watford in the FA Cup - and inability to cope with many of the wingers that he came up against saw large amounts of criticism come his way, and seemingly led to academy graduate Lewie Coyle being given his chance in the latter stages of the season.
And with Coyle showing glimpses of real quality when he has been given the opportunity, while Berardi seems to maintain a consistency that Leeds' defence have desperately needed this term, it is surely unlikely that Wootton would receive many chances next season anyway.