The broadcaster says the missing episodes, and two others, were found in the storeroom of a television relay station in Nigeria.
"Doctor Who" was first broadcast in 1963 and remains one of the BBC's most popular programs.
Some early episodes were lost because the broadcaster wiped the tapes clean for re-use.
The BBC says the lost episodes were tracked down by tracing records of overseas shipments of BBC tapes for transmission.
The recovered episodes date from 1967 and 1968 and feature Patrick Troughton, the second of a dozen actors to play the show's time-traveling alien hero.
They consist of most of two six-part stories: "The Web of Fear" and "The Enemy of the World."
They will be offered for sale on iTunes from Friday, and later on DVD.
Almost 100 episodes of the series are still missing.
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