His first was to Austria two years ago, where he found a strongly critical and somewhat apathetic Catholic flock.
In order not to antagonise his Czech hosts the Pope deliberately chose not to mention some common contentious issues of Catholic teaching such as that on abortion, or same-sex marriages, or the problems of dealing with paedophile priests and compensating their victims, which have dominated his visits to other parts of the world.
During his three-day visit to the Czech Republic, he had to tread carefully through difficult historical, political and linguistic minefields.
Because of persisting bad memories of the country's World War II Nazi occupation he could not use his native German in public - except for a few words addressed quite properly to a group of German pilgrims who crossed the border to see him.
Without his predecessor John Paul II's broad knowledge of Slavonic languages, in order to maintain political correctness Pope Benedict decided to speak in English or in Italian most of the time.
At his final Mass near Prague - attended by tens of thousands of young Czechs, most of whom had memories neither of German nor Communist rule before the Velvet Revolution of 1989, he started the liturgy in Latin, and the congregation quickly took up the responses in Czech.
What we were seeing was the new slimmed-down Czech church, a small but well-organised minority of believers coexisting within a much larger community of agnostics and atheists in a country that, to a large extent, no longer believes in God.
There were no portraits of the Pope in the streets of Prague, no yellow and white Vatican flags or bunting on display.
It was just a big national holiday weekend and many Czechs I spoke to were not even aware of the papal visit.
With celebrations planned for November (to mark the 20th anniversary of the Velvet Revolution) uppermost in everybody's minds, the Pope vigorously reminded his audiences of the iniquities of the Communist regime's suppression of religion.
The closing of the churches, the arrest of priests and monks and the propagation of an atheist creed had inflicted grave wounds on the ancient Christian traditions of the lands of Bohemia and Moravia, he said.
You only have to look at the Czech capital's skyline, spiked with soaring gothic church spires, and observe the number of Baroque churches and palaces dating from the time of the counter-reformation, to understand how Prague's architecture is out of sync with today's highly secularised Czech state.
The towering centre-piece of the city, the Cathedral of Saint Vitus, inside the spectacular castle complex, is crammed with noisy camera-wielding tourists, not hushed worshippers.
I saw no candles burning at the cathedral's side altars on the national holiday. Although religious services are allowed to be held, the building is still a state-owned museum, just as in Communist times.
The Catholic Church lost the legal battle to recover its original title to the building, which was constructed over a period of nearly 1,000 years and finally completed and consecrated only in the early 20th Century.
The Catholic Church in Czech-speaking lands has clearly suffered lasting damage.
Cardinal Miloslav Vlk, the head of the local Catholic church - who is due to retire shortly - went on national television during the Pope's stay to lament that in the two decades he has been in office since the fall of Communism, he has achieved practically nothing - neither compensation from the state for seized Church property, nor a proper treaty regulating relations with the Vatican.
He blamed local politics.
During Benedict XVI's visit the Pope's number two, Cardinal Tarcisio Bertone, the Vatican secretary of state, told Cardinal Vlk not to push the Czech state authorities too hard for money at a moment of huge economic difficulties in the countries of Central and Eastern Europe.
This was certainly welcome news for the Pope's hosts, but rather disappointing for the Czech bishops.
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