Czech President Petr Pavel honoured the Polish Pope on Monday in Prague with the Order of Tomas Garrigue Masaryk first class "in memoriam".
John Paul II received the order "for his outstanding services to the development of democracy, humanity and human rights".
The Order of Masaryk, named after the founding president of Czechoslovakia, is the second highest order of the state after the Order of the White Lion.
The Apostolic Nuncio to the Czech Republic, Archbishop Jude Thaddeus Okolo, accepted the award at the traditional ceremony on the occasion of the bank holidays on Monday.
"His Holiness Pope John Paul II (Jan Pavel II in Czech), whose civil name is Karol Jozef Wojtyla", played an "extraordinary role at the time of the fall of the communist regimes in Central and Eastern Europe", according to the brief introduction read out by the recipient of the order.
Among the 56 people honoured this year is the Catholic priest Josef Suchar, parish priest and co-founder of the "Neratov" (Bear Forest) association.
The organisation is dedicated to renewing the pilgrimage system in the once German-populated village on the Polish border, as well as helping people with disabilities and disadvantaged children.
Suchar received the Masaryk Order fourth class, as did the Pope, for "outstanding services to the development of democracy, humanity and human rights".