The actor, who first played the role on television in 2005, will feature in 12 episodes of the series, which will be released next year.
The Doctor Who: The Ninth Doctor Adventures series will be released across four box sets which will be available on CD and vinyl, as well as for digital download.
Eccleston said: “After 15 years, it will be exciting to revisit the Ninth Doctor’s world, bringing back to life a character I love playing.”
Information about other cast members, writers and story details has not yet been released.
The series is being created by Big Finish Productions in association with BBC Studios.
The first volume of the series will be available in May 2021.
Big Finish chairman Jason Haigh-Ellery said: “I first talked to Christopher about returning to the role of the Doctor at a fan convention in February this year.
“Christopher said he was enjoying meeting the fans and was pleased that his Doctor was remembered so fondly.
“I am so pleased that Christopher has decided to return to the role with us – and I’m excited to welcome him to the Big Finish family as we discover the new adventures of the Ninth Doctor.”