Church helped save the Castro brothers in the 1950s, then was sidelined by the atheist state.

After a failed attack on a military barracks by fighters led by Fidel Castro ended in disaster in 1953, soldiers hunted down the surviving rebels. Horrified by the bloodshed, the Archbishop of Santiago interceded with authorities to save the rebel leader and his brother Raúl, now the president of Cuba, from certain death. It was one of many dramatic incidents involving the two Castro brothers—who attended Jesuit school—and the Catholic Church, the oldest institution on this communist island. The relationship between the Castros and the church could become more important in shaping the island’s near future. The church helped broker the recent restoration of diplomatic relations between Cuba and the U.S. and is the only significant independent organization in a one-party state.

On Sunday, the current head of the church, Pope Francis, met with Fidel Castro and exchanged gifts, hours before a half-hour private meeting with Raúl. The subjects of those meetings weren’t disclosed publicly. For its part, the church is working for reconciliation between the U.S. and Cuba, and among Cubans themselves. “The church in Cuba has opted to work for a soft landing,” Miami Archbishop Thomas Wenski said earlier this month. The archbishop brought a delegation of some 200 Americans, many of them born in Cuba, to the island for the papal visit. “The church understands that to have a peaceful transition and not chaos, Cuba needs reconciliation,” he said. Raúl Castro met Francis for the first time this year at the Vatican, where he pronounced himself to be a fan of the prelate who has played a key, behind-the-scenes role mediating the détente between Cuba and the U.S. “I read all of the pope’s speeches,” said Mr. Castro after the meeting. “If he continues to speak like this, I assure you, I will begin to pray again, and return to the church. And I’m not joking.” As children, the Castro brothers attended the island’s most prestigious preparatory school, the Jesuit-run Colegio Belen in Havana. Fidel, the older brother, was a brilliant student, former teachers and classmates told his biographers. Not so much Raúl, who withdrew from Belen within a year, according to Brian Latell, a Cuba analyst at the Central Intelligence Agency who wrote a psychological study of the brothers in his book, “After Fidel.” The Jesuits recognized Fidel’s leadership abilities early on, according to Mr. Latell, and sought to infuse him with Catholic values. Teachers didn’t consider “Fidel promising material for a religious vocation,” Mr. Latell says. “But their next most important mission was to train Cuba’s future political leaders.”

At Sunday’s meeting, Pope Francis gave Fidel Castro a book and two compact discs with sermons and songs by the late Father Armando Llorente, Mr. Castro’s mentor at Belen, who was exiled in 1961 and died in Miami. In a 2007 interview with the Spanish news agency EFE, Father Llorente said Mr. Castro’s school years were the best of his young life because until then “he didn’t feel loved by anyone.” In contrast, according to Mr. Latell, the Jesuit instructors found Raúl to be apathetic and disinterested in studying at Belen, and he left the school after a few months. And it was Raúl Castro, as defense minister in his brother’s new revolutionary government, who converted the Jesuit school into a military academy. Like the majority of Cubans, most Catholics at first widely supported Mr. Castro as he fought to oust the late dictator Fulgencio Batista.

But relations with the church soured when it became clear Fidel Castro intended to radicalize the revolution and align Cuba with the Soviet Union. In August 1960, the Cuban bishops issued a collective letter condemning communism. Mr. Castro saw the letter as a gauntlet thrown down by the church. During the next decade, the government declared the state to be atheist, nationalized education and confiscated the church’s schools, including Belen. Many priests, nuns and brothers were expelled from the country. Others were forced to go to work camps

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