She had lived in virtual isolation since 1948 in an old convent in the central Portuguese city of Coimbra that houses the order of the Carmelita Sisters where she dedicated her life to prayer and meditation.
Lucia de Jesus dos Santos, born on March 22, 1907, in recent years suffered from blindness and deafness.
She died at the convent, the station said citing a spokeswoman for the order.
Her body will be laid out in Coimbra's cathedral on Tuesday for mourners to pay their last respects, with the funeral scheduled for Wednesday.
Sister Lucia was just ten when she and her two cousins, Francisco Marto and his sister Jacinta, said they saw the Virgin for the first time in a field near the town of Fatima on May 13, 1917.
Lucia, the only one of the three children who was able to hear what the Virgin said, wrote two memoirs about the series of apparitions which occured throughout 1917.
The apparitions made Fatima one of Catholicism's most revered sites and thousands of faithful flock to a shrine which has been built on the site where the apparitions are said to have taken place each year.
Pope John Paul II attributes to Our Lady of Fatima his survival of an assassination attempt in 1981 and has since then visited the shrine several times.
Sister Lucia last spoke in public in May 2000 when the pope travelled to Fatima to beatify Francisco and Jacinta.
You could have fooled me.
The secular news releases fail to say that Sister Lucy was the greatest visionary of modern times, having had the privilege of personal, (and publicly witnessed), visitations from the Mother of Our Lord and being the conduit of Our Lady's call for the world to convert and return to prayer.
Along with these calls to conversion ominous warnings of great chastisements were conveyed through Sister Lucy should Mary's words be ignored. Those who have studied the visions and prophesies of Fatima know that several of these 'chastisements' have already occurred, along with the foretold 'signs' that were to precede them.