Reece Staples, 19, was arrested on suspicion of causing criminal damage after police were called to a disturbance in the Basford area of Nottingham.
The former Nottingham Forest midfielder was then taken to Oxclose Lane Police Station where he was to be held overnight.
Officers checked his cell at around 5am on Sunday and found him to be 'unwell'.
It is thought an ambulance was then called, but Staples was pronounced dead on his arrival at hospital.
The teenager signed for Carlton Town FC in October last year, after being released by Forest.
He had made his way up through the club's academy system making regular appearances for the under-18 and reserve teams.
A post-mortem examination did not identify any evidence of injuries that may have contributed to his death.
The Independent Police Complaints Commission has now launched an investigation.
It will consider what information Staples gave to police about his health and what actions were taken.
IPCC Commissioner Amerdeep Somal said on Sunday: "The investigation will look at all the circumstances in the lead up to this man's death when he died in the early hours of this morning.
"This will include how police dealt with information they received relating to the deceased's health and wellbeing."
A spokesman for Carlton Town FC confirmed Staples had died, but said the club would not be issuing a statement