Officials believe Lawrence Phillips, 40, killed himself early on Wednesday.
In the 1990s, he was a star player at the University of Nebraska, making him a sought-after rookie in the NFL.
Phillips played for the St Louis Rams, Miami Dolphins and San Francisco 49ers until 1999, but he was plagued by trouble on and off the field.
After his NFL career, Phillips continued to have problems with the law.
Eventually, he was sent to prison after being convicted of assault for driving his car into a group of teenagers.
In another case, he was convicted of assaulting a former girlfriend.
Phillips, who was serving a term of more than 30 years, had been placed in a cell alone after he was accused of killing his former cellmate.
On Tuesday, a judge found that there was enough evidence to try Phillips in the death of Damion Soward, 37.
It is unclear how he took his own life.
"He was an intelligent person and had some good qualities," Tom Osborne, his coach at Nebraska, told the Associated Press news agency.
"Yet he had some anger issues and couldn't overcome the demons in his life.''
A former US professional football player whose career was cut short by disciplinary problems has been found dead inside his California prison cell.