The omission of Colin Worrall, who is standing in the Bransholme West Ward for Yorkshire First, emerged during the verification process.
The council said the error had affected 168 ballot papers
It is a second ballot error in the city. Two candidates for the Hull East parliamentary election were left off postal ballots sent out in April.
Hull returning officer Ian Anderson said the latest error had been made by the print and distribution company.
"The total number of votes cast was 2,674," he said.
"Given the very limited numbers affected, the decision has been made to continue with the election and the count as normal."
A candidate for elections to Hull City Council has been left off some ballot papers.