Police had arrested Andallur Atholi Sudhirr, an uncle of the 13-year-old girl, from nearby Thalassery railway station last night and a local court remanded him in judicial custody today, police said.
The accused was taken to Kannur Central jail but before being lodged there, Sudhir swooned and was immediately taken to district hospital, where doctors declared him dead, police said.
Sudhir, a physically challenged person, had lost his legs in an accident a couple of years back.
The girl's father, her 15-year old brother and another uncle, have already been arrested for raping the girl.
The shocking incident came to light recently when the eighth standard student of a local school was seen crying and refused to go home even after school hours.
When one of her teachers enquired, the petrified girl narrated her plight, following which a complaint was registered.
The brother has been sent to juvenile home while the other two were produced in court and remanded to judicial custody.
The girl told police that she was sexually assaulted by the three since she was in her sixth standard.
The victim has also told police that her elder sister, who had committed suicide two years ago, had also been raped.