The actor, who was killed off in the Caribbean detective drama at the start of the most recent series, will star as a villain opposite Peter Capaldi in the new series, which is set to air later this year.
Speaking abut bagging the role, he said: "As a committed Whovian I cannot believe my luck in joining the 12th Doctor for one of his inaugural adventures.
"My only worry is that they'll make me leave the set when I'm not filming."
Steven Moffat, he show's executive producer, added: "Mark Gatiss has written us a storming villain for his new episode, and with Capaldi in the Tardis, we knew we needed somebody special to send everybody behind the sofa.
"And quite frankly, it's about time Ben Miller was in Doctor Who."
The actor rose to fame as half of comedy duo Armstrong and Miller before landing successful roles in dramas, including Primeval and Death In Paradise.
His comedy partner Alexander Armstrong has already appeared in Doctor Who in the 2011 Christmas Special, taking on the role of Reg Arwell.
Meanwhile, Moffatt recently opened up about what fans can expect from Peter Capaldi's portrayal of the iconic character.
The writer and producer said: "Scottishness. I think that’s the main thing.
"I mean watching him, and I just watched episode two actually, you don’t go around thinking this is an older bloke as The Doctor, particularly.
"You just think my God, he’s Scottish. And doomed dialogue doesn’t half sound great in Scottish. You say the world’s about to end in a Scottish accent, and you really believe it."