Bulger, 89, was arrested on October 30 in Hazelton, West Virginia, USA on a day after he was taken there.
His injuries occurred when he was "attacked by others," the document said. The approximate time between the beginning of his injury and death is given as "minutes".
The authorities have not declared Bulger dead by 09:04, the death certificate says.
Bulger, who has escaped federal custody 16 years before his arrest in June 2011, spent the rest of his life in prison for a litany of crimes, including his role in eleven murders.
He was sentenced to two more life sentences in November 2013. He was the architect of a criminal enterprise that, according to a federal judge, committed "inscrutable" acts that terrorize a city.
A federal jury convicted Bulger of 31 counts this year, including raids, extortion, money laundering, drug trafficking and drug trafficking.
The jury found him guilty in eleven murders from 1973 to 1985.