The news comes after the BBC announced it had already given the go-ahead to a second series following the success of Saturday's first episode, which was seen by more than 10 million viewers.
Eccleston, who admitted he found the show's filming schedule "gruelling," decided to leave over concerns of becoming typecast. "The audience’s response for the new Doctor Who has been incredible and I am really proud to be part of it," he said in a statement. "I hope viewers continue to enjoy the series."
Unusually, the BBC has confirmed it is "in talks" with Casanova star David Tennant as a possible replacement.
Eccleston's final appearance will be in a special episode this Christmas.