The former Crewe Alexandra coach, 69, was serving a 34-year sentence after being convicted of a number of child sex offences.
A spokesman for the Ministry of Justice said: “Prisoner Barry Bennell died at HMP Littlehey on September 16.
“As with all deaths in custody, the Prisons and Probation Ombudsman will investigate.”
Bennell, also known as Richard Jones, was jailed for 30 years in 2018 after being convicted of 52 child sexual offences against 12 boys.
He was ordered to serve an additional four years in 2020 after pleading guilty to other offences against two boys.
When he was sentenced at Liverpool Crown Court in 2018, Recorder of Liverpool Judge Clement Goldstone QC said he “may well die in prison”.
His final prison sentence, in 2020, was the fifth time he had been jailed.
At that hearing, the court was told he had a detached retina after being attacked in prison and was in remission from cancer.
Bennell, a former Manchester City scout, abused boys he coached in the 1970s, 1980s and 1990s.
Bennell was first jailed in Florida in 1994 for raping a British boy on a football tour in America, before going on to face prison sentences in Britain in 1998, 2015, 2018 and 2020.
Following his convictions in 2018, more than 80 other alleged victims came forward to report abuse by him.
At his sentencing hearing in 2020, Owen Edwards, prosecuting, said the case would be the final prosecution after a decision to proceed only with cases involving the most serious offences.
He said Bennell was responsible for “industrial sexual abuse of boys”, as well as being instrumental in forging the careers of several international footballers.
In court during his 2018 trial, Bennell’s victims told how he had a “power hold” over them as they dreamed of becoming professional footballers.
He was said to have been treated like “God” at Manchester City’s Maine Road ground.
He abused the boys at his homes, where he had arcade games and exotic pets including a puma and a monkey, but also on trips away and in his car while on the way to and from training.