The actor, best known as one half of comedy duo Armstrong and Miller and for starring in ITV drama 'Primeval', will appear opposite Peter Capaldi when he kicks off his first series as the new incarnation of the Time Lord this autumn.
Ben enthused: "As a committed Whovian I cannot believe my luck in joining the Twelfth Doctor for one of his inaugural adventures. My only worry is that they'll make me leave the set when I'm not filming."
The 48-year-old star has been cast as the baddie in an episode written by Mark Gatiss and rose to the occasion by putting on a terrifyingly villainous performance.
Steven Moffat, the BBC One show's head writer and executive producer, commented: "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's comedy partner Alexander Armstrong has previously joined the last of the Time Lords on his intergalactic adventures during the 2011 Christmas special.
Ben was last seen as DI Richard Poole in the first two series of the BBC's 'Death In Paradise'.