Officers were called to Kingsley Road in the early hours of Thursday morning (March 9).
Police say that 'at some point' the 16-year-old boy became unwell and was taken to the Countess of Chester Hospital but sadly died last night.
Next of kin have been informed and a Home Office post mortem is taking place.
The death is 'not suspicious' but is being treated as unexplained and detectives are looking at how he became unwell.
Five teenagers were arrested and have since been bailed.
Inspector Ian Stead, of Ellesmere Port, said: “We are aware of rumours circulating of a boy being stabbed. I’d like to reassure the community that this is not the case. This is an isolated incident involving teenagers who were known to each other.
“Our thoughts are with the family of the boy.”
House-to-house and forensic enquiries have been carried out in the area.