Tranmere boss Little said: "He hasn't been able to gain a regular place in the team this season so we have given him the opportunity to move on with his career.
"He is someone I have known for a long time who has been a very good player for me and I wish him every success in the future."
Whitmore was with City between 1999-2002 before being released, and rejoined former Tigers manager Little at Tranmere, via a spell at Livingston, in 2004. He played in 37 games last season, scoring five times, as Tranmere just missed out on promotion. One of those games was an ill-fated attempt at being an emergency goalkeeper when Rovers came to Hull, letting in five goals in a 6-1 defeat after coming on at half time when both goalkeepers in Tranmere's matchday squad suffered first half injuries.
Fellow Jamaican Ian Goodison, who came to Hull City at the same time as Whitmore, remains a regular at Prenton Park, where ex-Tigers Steve Wilson and Delroy Facey also currently ply their trade.