Worshippers have flocked to the Coimbra cathedral in Portugal to pay their last respects to Sister Lucia, who claimed to have seen the Virgin Mary in 1917.
A service is being held for Sister Lucia at Coimbra's cathedral
She died on Sunday, aged 97 - the last of three shepherd children who turned the town of Fatima into a pilgrimage site after telling of their visions.
Her body was taken from a convent in Coimbra to the city's cathedral for a funeral service on Tuesday.
Portugal is holding a day of national mourning for Sister Lucia.
Flags are flying at half-mast and politicians have suspended campaigning for this weekend's general election.
In a condolence message, Pope John Paul II said he had "always felt lifted by the daily gift of her prayers, especially in difficult and testing moments of suffering".
Thousands of mourners have paid their respects in Coimbra
The pontiff made three pilgrimages to Fatima.
Sister Lucia de Jesus dos Santos will be buried at the Carmelite convent in Coimbra, in central Portugal.
Her remains will be transferred in a year's time to the Fatima shrine.
At a ceremony there in May 2000 the Pope beatified Sister Lucia's younger cousins, Francisco Marto and his sister Jacinta, who died of flu within three years of their visions.
The Vatican is expected to start the process of beatifying Sister Lucia too.
The cousins were tending sheep when they saw the visions
The Virgin Mary is said to have revealed prophecies of key 20th-Century events, including the end of World War I, the start of World War II and the rise and fall of Soviet communism.
The Church believes the third "secret", not unveiled until 2000, foretold the attempted assassination of Pope John Paul on 13 May 1981, the anniversary of one of the 1917 apparitions.
Sister Lucia's death had been anticipated for some time.
"She had been weak for several weeks and had not left her cell," said Coimbra Bishop Albino Cleto.
Sister Lucia was the only one of the three children who claimed to have heard clearly what the Virgin Mary said.
The cousins were tending sheep when they saw the visions.
Sister Lucia went on to write down what she had been told.
The first two parts of the prophecy were known for decades and interpreted as predicting the world wars. But the third prophecy was kept secret and sparked much speculation about its content.
When the Vatican revealed its interpretation of the vision, the Pope credited the Madonna of Fatima with his survival following the 1981 attempt on his life by Turkish gunman Mehmet Ali Agca in St Peter's Square.