The Prison Service said the 44-year-old's next of kin has been informed. It happened in the early hours of Saturday morning.
The PSNI, Coroner and Prisoner Ombudsman have launched investigations into the death.
The Head of the Prison Service Ronnie Armour said: "I would like to extend my sympathy and that of the Northern Ireland Prison Service to the family of the prisoner who has died in Magilligan.
"My thoughts are with them at this difficult time."
The Northern Ireland Prison Service has confirmed that a prisoner has died in custody at Magilligan Prison in County Londonderry.