It was discovered on Tuesday on an embankment by the city's Victoria Dock.
Humberside Fire and Rescue Service said it was called at 22:08 GMT and rescued the seal using a salvage sheet.
The pup has been named Basil and is now being cared for at the Sea Life Centre in Scarborough.
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A stranded seal pup found near a former Hull dock has been rescued by firefighters and the RSPCA.