The Education Policy Institute said the figures, which show the vast majority of pupils across England were absent, confirm children have suffered "significant learning loss" during the coronavirus lockdown.
Since asking schools to close on March 20 to all but vulnerable children and those of critical workers, the Department of Education conducted a weekly survey of schools, colleges and nurseries to track attendance rates.
The final survey on July 16 shows 65% of schools were open in Sheffield with 11% of the area's children present.
The area had a lower attendance than the national rate for England of 16%
Approximately 1.5 million children were in school on the day throughout the country – down from 1.6 million a week before, which was the largest number since lockdown began.
Local data is only available for the most recent survey.
The EPI think tank said the most disadvantaged pupils are likely to have been hit the hardest.
Natalie Perera, executive director and head of research at the organisation, said getting students back into the classroom in September is vital, but comes with a number of risks, particularly around social distancing.
She added: "Schools will have gained experience from having some pupils present since March, but the reality is the situation next month will be vastly different to what we have seen so far, with an array of additional challenges.
"Big questions remain about the level of risk that school staff, pupils, and their families are being asked to take."
The Government asked schools across England to welcome back children in nursery, reception and years 1 and 6, from June 1.
Two weeks later, year 10 and 12 students were allowed in to supplement their learning from home, but numbers were limited to reduce the risk of infection.
Plans for all primary pupils to return were dropped but schools were allowed to make their own decision about admitting more children.
On July 16 in Sheffield, 60% of secondary schools were open, compared to 55% of primary schools – though any which failed to respond to the survey were assumed closed.
Attendance rates that day ranged from 25% in year 6, to 8% in nursery.
Will Millard, head of engagement at The Centre for Education and Youth, said: "These figures are a stark illustration of just how profoundly children's educations have been hit by the pandemic.
"Far from being a 'great leveller', the virus has hit some areas far harder than others.
"It highlights the enormous challenge schools face as they re-open."
Prime Minister Boris Johnson said he had “no doubt” that schools would be able to re-open, but stressed the need for discipline to prevent the spread of the virus.
Education Secretary Gavin Williamson has insisted that research showed “little evidence that the virus is transmitted at school”, but Health Minister Edward Argar warned against reading too much into the unpublished work by Public Health England.