The 21-year-old centre-half, who can also play in either full-back position, has experience of playing in the Champions League as well as featuring in last season's Capital One Cup.
Wootton has previously had spells on loan with Tranmere, Nottingham Forest and two spells with Peterborough.
Leeds manager Brian McDermott is happy to land a player he feels will be a long-term asset at Elland Road.
McDermott said: "I'm delighted to have agreed the signing of Scott Wootton on a three-year deal.
"He's a player who has played in the Champions League and someone we feel will develop with us in the coming years.
"I want to say thanks for the owners in doing the deal and bringing another young player to help us go forward."