Fishermen Edwin Stokes and Allen Longland looked on in disbelief as the relic was pulled up from the seabed along with their usual haul.
The pair landed the skull as they fished in their boat, the Bolt Head Queen, in the Emsworth Channel, off the south eastern tip of Thorney Island.
The skull was covered in anemones and still had four teeth intact, although the jaw bone was missing.
Mr Stokes said: 'I was surprised – I have been fishing there for 30 years and I have never seen anything like that come out with a dredge.
'The first thing we said was "You don't often catch one of these".
'It looked quite old to me. I think the fact that there are still teeth shows it has been preserved or buried.
'If it had rolled around on the sea floor, it wouldn't have teeth.
'With the rough weather there were strong swells so perhaps that is what uncovered it.'
The skull was handed in to Chichester Harbour Conservancy office, based at Itchenor, near Chichester, and staff there have handed it to the police.
Sussex police are now conducting an investigation to find out where the skull may have come from and the possible identity.
A spokesman said it will be examined by a forensic anthropologist to determine its age before they decide what to do next.
They are not treating it as suspicious.
Ali Beckett, publicity and information officer for the conservancy, said human remains were extremely rare in the harbour.Bones have been dredged up in the past as an ancient burial site is believed to be situated near West Wittering.
But she said: 'We have had nothing as intact as this.'
Mr Stokes, of Almodington, near Chichester, said: 'People are saying it could have been an airman shot down during the war who was never reported. Who knows? It's a complete mystery at the moment.'
Archaeologist Margaret Rule, who led the project to excavate the Mary Rose, believes the skull could be several hundred years old.
She said human remains of French prisoners of war had been washed up at Portchester, but she had never seen them at Thorney Island.
She added: 'I can't think of anything other than a burial at sea. It has probably washed up from deeper water.
'The teeth look fairly well grounded down, which suggests some age. There's nothing to suggest it was recent.
'Signs of a brow ridge would suggest it is male.'
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