Once Russia's richest man, Khodorkovsky has been convicted in Russia of evading taxes and stealing oil from his own company. He is due for release in 2014.
His case is seen as President Vladimir Putin's punishment for Khodorkovsky's political ambitions and support for the opposition.
The board of the USD 100,000 award said today Khodorkovsky is being recognized for 'courage in promoting civil society values," building foundations of economic freedom and "unwavering struggle for justice and human dignity."
Khodorkovsky's son Pavel is to receive the award on Sunday in Gdansk, where Walesa founded Solidarity in 1980. It later ousted communism from Poland, and Walesa won the 1983 Nobel Peace Prize.