The 24-year-old has put pen to paper on a two-year deal at Roots Hall and is reunited with manager Phil Brown, whom he played under during the pair's time at Hull.
Brown told Southend's official website: "Will had such a fantastic work-rate and desire to succeed and I remember that extremely well from our time at Hull.
"I'm delighted he has joined the club. He's another player, just like John White, who fits the bill perfectly and I'm looking forward to working with him again."
Atkinson, who made 57 appearances for Bradford during their promotion and Capital One Cup final campaign last season, made just eight first-team appearances at first club Hull.
He had loan spells at Port Vale, Mansfield, Rochdale, Rotherham and Plymouth before joining Bradford, initially on loan, in July 2012.