He was taken to Aberdeen Royal Infirmary after he was found in the stairwell of flats on Sunday morning.
It has been confirmed tonight that the ex-Aston Villa player has lost his battle following his collapse.
The 54-year-old took charge of the club in 2003, guiding the Pools to the Division Two play-offs before losing out to Bristol City.
He spent two years at Victoria Park before resigning for family reasons.
Police say his death is not being treated as suspicious but confirmed their inquiries are continuing.
“We are heartbroken,” read at Hartlepool statement. “Everyone at the club is absolutely devastated to hear that former boss Neale Cooper has died at the age of 54.
“Our thoughts and condolences are with his family and friends at this time.”
Pools have been inundated with messages, many calling Cooper a “legend” with footballer Phil Turnbull calling his former manager the “most charismatic man you could ever meet”.