The news comes after Pope Francis recently made the surprise announcement that Benedict, formerly known as Cardinal Ratzinger, was “very sick” and asked for people to keep him in their prayers.
Pope Emeritus Benedict XVI, whose health had been deteriorating became the first pope in 600 years to resign, back in 2013, and he chose to live out his retirement in seclusion in a converted monastery in the Vatican.
He famously visited Scotland in 2010, being greeted by crowds in Edinburgh and Glasgow, and delivering Mass at Bellahouston Park.
A statement from Vatican spokesman Matteo Bruni said: "With pain I inform that Pope Emeritus Benedict XVI died today at 9:34 in the Mater Ecclesia Monastery in the Vatican. Further information will be released as soon as possible."
Benedict stunned the world on February 11 2013 when he announced that he no longer had the strength to run the 1.2 billion-strong Catholic Church that he had steered for eight years through scandal and indifference.
His dramatic decision paved the way for the conclave that elected Pope Francis as his successor.
The two popes then lived side-by-side in the Vatican gardens, an unprecedented arrangement that set the stage for future "popes emeritus" to do the same.
A leading Scottish archbishop today recalled the "honour" of working closely with Benedict.
Leo Cushley, who has been Archbishop of St Andrews and Edinburgh since 2013, accompanied him on international trips in his capacity as the head of the English language section of the Vatican Secretariat of State between 2009 and 2013.
That included trips to Malta, Cyprus and the UK in 2010.
In 2012, he took on an additional ceremonial position at the Vatican where he assisted Benedict when he received visits from prominent dignitaries.
The archbishop said the 2010 papal visit to the UK was a personal highlight.
Benedict met the Queen at the Palace of Holyroodhouse in Edinburgh before travelling to Glasgow for an open air Mass at Bellahouston Park.
It was the first papal visit to Scotland since Pope John Paul II in June 1982.
Benedict also had lunch with the archbishop at the official residence of the Archdiocese of St Andrews and Edinburgh.
Mr Cushley told BBC Scotland: "I had never seen anything like it. I don't think the Pope had seen anything like it either as he was welcomed there.
"It was a wonderful day."
He said the former pope's visit captured the attention of many people in Scotland.
He added: "It was a lovely, happy occasion where not only the Catholics of Scotland welcomed their pope, the Bishop of Rome, many other people did that too.
"I could not have imagined it any better and, the way it worked out, I was very proud of the way my country welcomed Pope Benedict in their midst."
He also recalled the "real kindness" of Benedict as he greeted school children in Edinburgh.
Mr Cushley added: "I had the honour of working with him closely towards the end of his time as pope, and I got to see this for myself.
"He was a good priest and a meticulous scholar. He was also quietly kind and available to people.
"His scholarship and his writing will be remembered in time to come, as will his humility and humanity.
"He will be deeply missed."
The former Cardinal Joseph Ratzinger had never wanted to be pope, planning at age 78 to spend his final years writing in the "peace and quiet" of his native Bavaria.
Instead, he was forced to follow the footsteps of the beloved St John Paul II and run the church through the fallout of the clerical sex abuse scandal and then a second scandal that erupted when his own butler stole his personal papers and gave them to a journalist.
Being elected pope, he once said, felt like a "guillotine" had come down on him.
Nevertheless, he set about the job with a single-minded vision to rekindle the faith in a world that, he frequently lamented, seemed to think it could do without God.
"In vast areas of the world today, there is a strange forgetfulness of God," he told one million young people gathered on a vast field for his first foreign trip as pope, to World Youth Day in Cologne, Germany, in 2005. "It seems as if everything would be just the same even without him."
With some decisive, often controversial moves, he tried to remind Europe of its Christian heritage. And he set the Catholic Church on a conservative, tradition-minded path that often alienated progressives.
He relaxed the restrictions on celebrating the old Latin Mass and launched a crackdown on American nuns, insisting that the church stay true to its doctrine and traditions in the face of a changing world. It was a path that in many ways was reversed by his successor, Francis, whose mercy-over-morals priorities alienated the traditionalists who had been so indulged by Benedict.
Benedict's style could not have been more different from that of John Paul or Francis. No globe-trotting media darling or populist, Benedict was a teacher, theologian and academic to the core: quiet and pensive with a fierce mind.
He spoke in paragraphs, not soundbites. He had a weakness for orange Fanta as well as his beloved library; when he was elected pope, he had his entire study moved - as is - from his apartment just outside the Vatican walls into the Apostolic Palace. The books followed him to his retirement home.
"In them are all my advisers," he said of his books in the 2010 book-length interview "Light of the World." "I know every nook and cranny, and everything has its history."