The 37-year-old, from Blanchardstown in west Dublin, went missing in October and some of his body parts were found in the townland of Mayne, Co Meath, early last month.
However, his head was still missing and gardaí had been carrying out searches of nearby areas when the discovery was made on Saturday.
Officers found a skull on open ground in Clonee while searching the area and gardaí believe it belongs to Mr Gaffney, who was dismembered by his killers.
The skull was taken to the nearby James Connolly Hospital and will now undergo DNA tests and an autopsy to identify it. Gardaí hope it might also provide new evidence as to how Mr Gaffney was murdered and who carried out the murder.
Last night, gardaí could not say exactly how long the DNA testing process would take but results are not expected within the next week.
As yet, no-one has been arrested in connection with Mr Gaffney’s death and gardaí are seeking a motive for his killing.
The Dubliner had a number of convictions for drugs offences. One theory is he was killed by a drugs gang.