The former oil tycoon left the Segezha prison colony on Friday after Putin signed a decree authorising Khodorkovsky's release.
Putin reportedly said his decision to grant Khodorkovsky clemency was "guided by the principles of humanity."
Hours later, Khodorkovsky flew to Germany where his mother is undergoing treatment, though reports said that it is not clear whether he intends to stay in the country.
Once claimed as Russia's richest man, Khodorkovsky was arrested in 2003 on allegations of tax evasion and fraud at his oil company Yukos.
His arrest was seen as politically motivated one since it followed soon after he challenged Putin over top-level corruption.
--IBNS (Posted on 20-12-2013)