The first of the four series is available from today and features Christopher Eccleston as the Doctor.
Single episodes cost £1.89 and the entire 13-episode series can be bought for £19.99 through the iTunes Store.
Eccleston was replaced after one season by David Tennant, who joinedBillie Piper in the next series, which will appear on iTunes on 9 December.
The subsequent two series will be available on 16 December and 23 December. Freema Agyeman and Catherine Tate have also appeared in recent series.
Simon Danker, director of Digital Media at BBC Worldwide, said: "Doctor Who is one of the most popular and enduring brands on British TV and the new series has introduced the Time Lord to a whole new audience.