A man walking his dog reported seeing the body in the water at about 09:00 BST, Humberside Police said.
It was recovered from the water as an area near the pier gates was cordoned off by police.
The male body is yet to be identified and the force is appealing for anyone with information to contact them. Withernsea lies about 18 miles east of Hull.
The pier out into the North Sea was demolished more than 100 years, ago, but the gates were left standing on the promenade.
A body was washed up on a beach at Withernsea, East Yorkshire.