The Downton Abbey star will play a "pirate captain" on the sci-fi drama, according to The Sun.
"I am thrilled to be appearing in the new series," Bonneville was quoted as saying. "When I was a boy, the music and Jon Pertwee's Doctor had me peeking out from behind the sofa every Saturday."
He continued: "Although the pirate's demons are different to those of the young lad who watched through his fingers, they are no less terrifying. This new adventure is not for the faint-hearted."
Bonneville later wrote via Twitter: "No idea what the weather's like on earth this day in 2011 because I am elsewhere, IN THE ACTUAL TARDIS ACTUALLY (sic)."
The actor previously received a BAFTA nomination for his performance in 2001 film Iris and will reprise his role as Robert Crawley in a second series of Downton Abbey later this year.
The sixth series of Doctor Who is expected to launch on BBC One in the spring.