The 24-year-old midfielder helped the Bantams to promotion from League Two and the final of the Capital One Cup last season.
Atkinson links up once more with Southend boss Phil Brown, who managed him at Hull City.
"Will had such a fantastic work rate and desire to succeed," Brown told the club's official website.
"I'm delighted that he has joined the club. I'm looking forward to working with him again."
Atkinson made 57 appearances for Bradford last season.