Francis Moore, who was known as Father Paul Moore, was transferred from his cell in HMP Dumfries to the nearby Dumfries and Galloway Royal Infirmary after falling seriously ill.
The 85-year-old, who struck at various locations including a busy Ayrshire leisure centre between 1977 and 1996, died on Saturday.
Moore was jailed for nine years following a BBC investigation, but his sentence was later reduced by 12 months by appeal court judges sitting in Edinburgh..
Moore's crimes spanned more than 20 years and one of his victims was just five years old.
In November 2019 Moore was defrocked by the Pope, meaning he was cast out of the church and was no longer be able to call himself "father" or offer spiritual care.
The BBC investigation found that Moore had admitted in 1996 that he had abused more than one boy years earlier, and it was initially covered up by the then Bishop of Galloway, Maurice Taylor.
Bishop Galloway did not contact the authorities about Moore’s confession for eight months, sending him instead to a treatment centre in Canada.
He removed Moore from his parish in Prestwick, Ayrshire, and later sent him to Fort Augustus Abbey on the shores of Loch Ness, which was run by Benedictine monks. The church later bought him a retirement home in Ayrshire.
It was only when the victims came forward after the BBC documentary that the criminal case was brought and church leaders finally apologised to the victims.