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Brady was jailed for three murders in 1966 and later confessed to two more.
The 79-year-old had been held at Ashworth Hospital, a secure psychiatric unit in Merseyside, since 1985.
Brady and his lover Hindley, who died in prison in 2002, buried four of their victims in graves on Saddleworth Moor, near Oldham, Greater Manchester.
A Mersey Care NHS Foundation Trust spokesman said: "We can confirm a 79-year-old patient in long-term care at Ashworth High Secure Hospital has died after becoming physically unwell."
Brady, who was born in Glasgow but later moved to Manchester, was jailed at Chester Assizes for the murders of 12-year-old John Kilbride, Lesley Ann Downey, aged 10, and Edward Evans, 17.
Almost 20 years later, in 1985, he admitted to the murders of Pauline Reade, 16, and Keith Bennett, who was 12.
The children were killed after being abducted by Brady and Hindley between 1963 and 1965.
Brady never revealed where Keith's remains were buried. The boy's mother Winnie Johnson, who died in 2012, had repeatedly pleaded for Brady to do so.
Keith's brother Alan runs a website, Searching for Keith, in an ongoing attempt to locate his body.
Brady: The notorious murderer who refused to show remorse
Speaking about the case of victim Lesley Ann Downey, former police officer Norman Brennan told of the "grief and torment" he had seen on the faces of her mother and father.
He told BBC Two's Newsnight: "To know that your daughter was lost, alone and murdered and then actually her death was recorded, the grief can never ever be etched from your mind.
Brady never revealed where Keith Bennett's remains were buried
"Those two individuals, Myra Hindley and Ian Brady, they didn't just destroy five young children's lives.
"The... false hopes that they gave the families for over 50 years destroyed all of the families as well, even to this day."
Brady had been on successive hunger strikes since 1999, arguing he should be allowed to die, but had been force-fed because he was considered mentally ill.
He campaigned for several years to be moved from Ashworth to a Scottish prison where he would not be force-fed and would be allowed to die if he wished.
A Mersey Care NHS Foundation Trust spokesman said Brady had died at 18:03 BST on Monday.
The spokesman was unable to confirm the cause of Brady's death, but said he had been given oxygen for a while.
Brady was not found dead in his room, the spokesman said, but he was unable to confirm if anyone was with him when he died, adding: "Quite possibly. I don't know."
