Barry Johnston, 25, was rushed to hospital in Belfast on Friday.
He has been in Maghaberry prison since he was remanded in custody after appearing in court last Monday.
He is accused of raping a 74-year-old woman in Ballymena.
It is understood Johnston is being treated at the Royal Victoria hospital where his condition is described as critical.
A spokeswoman told UTV on Saturday night: "The Northern Ireland Prison Service could confirm an individual was taken to hospital from Maghaberry prison yesterday and remains under treatment”.