The council’s Director of Public Health Andy Kingdom said large numbers of people “squashed together” in the Walton Street fairground was a risk.
He added infection levels were expected to stay high through Autumn while hospitals remain under pressure, school pupils return and more people mix indoors.
It comes as the number of new coronavirus cases recorded in the East Riding fell from 1,401 between Wednesday, August 18 and Tuesday, August 24 to 1,275 the following week.
The East Riding’s seven day rolling rate of infections dropped from 408 to 372 per 100,000 people during the same period.
It also follows a warning from Fair organisers of higher than normal visitor numbers as it is the only event of its kind taking place outside London this year.
But Mr Kingdom said the amount of infections was at its highest since at least January despite the drop.
The director said: “I think the showmen at Hull Fair will do their best to make sure its a safe environment for those attending.
“But I’m worried because there will be large numbers of people being squashed together in close quarters, particularly at pinch points in the fairground.
“With the cancellation of the Nottingham Goose Fair it’s expected to be busier than normal.
“And it’s not just the Fair itself, they’ll be people meeting in groups in pubs and bars before and afterwards then travelling back home and taking coronavirus with them if they’ve caught it.
“I would advise anyone going to get tested before and afterwards and if you are positive before then self-isolate.
“I’d also recommend attendees wash their hands regularly, wear masks and socially distance where they can.
“Everyone has now had the chance to get a coronavirus vaccination and they’ve made their choice and there’s consequences to that either way.
“Large scale events, especially indoor ones, have the potential to be super spreaders and I imagine businesses will be taking the lead on asking for proof of vaccination and a negative test to keep visitors and staff safe.
“Going to these events unvaccinated would be like driving without a seat beat and the roads are still busy coronavirus wise.”
The director said his concerns about the Fair came as pupils return to school and people go back to work following summer holidays, increasing the risk of coronavirus spreading.
He added that came as around 72 beds in Hull Royal Infirmary and Castle Hill Hospital were currently occupied by coronavirus patients ahead of a “tough winter” for the NHS.
Mr Kingdom said: “We’re already seeing a rise in hospital admissions for other respiratory illnesses because people have been less exposed to them during the pandemic.
“And there’s the backlogs in hospitals, some patients have been waiting almost two years for some operations.
“So that plus the amount of people in hospitals with coronavirus and staff fatigue means they’re under extreme pressure.
“We’re no longer trying to put out every little fire of coronavirus, we’re now trying to stick to an acceptable level of burning because to do more would be too damaging to society.
“That’s the gamble we’re taking, getting the balance right is tricky and with the vaccine doing most of the hard work of combating coronavirus far more is down to personal responsibility.”
Article by Local Democracy Reporting Service reporter Joe Gerrard