Penistone Grammar leaders described their frustration at rising rates having recorded 52 new cases.
The school - which had just 13 cases up to June 20 - now has quadruple that figure which led to a mass testing programme being brought in this week to halt the virus’ spread.
The spike - which occurred between June 20 and June 28 - has predominantly affected the year ten group, which had 30 cases.
However, school bosses have also seen increases in years seven and eight, which contains youngsters between the ages of 11 and 13.
Principal Paul Crook said he felt sympathy for pupils who have had disrupted routines after taking the decision to close three classes this week.
“Between the period of June 20 and June 28, we have had a total of 52 confirmed cases of Covid-19 for students in our school,” he said in a statement.
“Of these cases, although 30 have been concentrated in year ten, in recent days we have also begun to see increasing instances of Covid-19 across all other year groups.
“This has resulted in a decision to close two classes in year seven, and a class in year eight, in an effort to restrict any further transmission of the virus.
“Over the past week we have once again seen our school community come together to support our young people, and while so many have shared messages of support with us, it is clear we share the same frustration that our children have missed too much over the course of the last 18 months.
“It seems incredibly unfair that they are, once again, facing further time out of school and away from face-to-face learning opportunities for reasons outside of their control.”
All groups - from year seven to 12 - have had periods of at-home ‘remote learning’ this week, something which will continue for the year eight pupils today and year ten today and Monday.
All other pupils must complete home testing or undergo lateral flow tests upon arrival at the school, then await a negative result before entering their classroom.
Letters were sent to parents and carers on Tuesday in relation to the increased cases.
Mr Crook added: “Given that there has been no respite from the pace of the spread of the virus over recent days, if we are to protect our students’ education for what remains of the final term of this academic year and do everything we can to make sure our students can go into the summer break free from self-isolation and Covid-19, so we must now introduce further decisive action.
“We have worked closely with representatives from Public Health England and Barnsley Council and can confirm that from Wednesday we supplemented the isolating of contacts and closing of classes, where appropriate, with the introduction of a mass testing programme.
“To implement this effectively and to give us the best possible opportunity to stop any further spread of the virus, it was necessary to make some short-term adjustments to learning this week.
“We apologise for the urgency at which we have had to put these arrangements in place, and the inconvenience this undoubtedly caused, but given the pace at which the virus is moving, it is necessary to act quickly.
“We are hoping that any short-term disruption will be offset by a longer-term gain.
“Mobilising the mass testing programme at such short notice has been a challenging task for the school, local authority and Public Health England representatives.
“I would like to take this opportunity to thank everyone for the support they are providing to the school at this challenging time - our staff remain committed to ensuring our students are supported to access an excellent educational experience at home and in school.
“Finally, I would like to thank our students, who remain resilient and resolute despite facing yet more adversity at the hands of the coronavirus pandemic, they make me proud every day.”
Julia Burrows, the town’s director of public health, praised the school’s quick response.
“We are seeing this impact across the borough and schools are affected as a result,” she said.
“Penistone Grammar School acted quickly to ensure the safety of pupils and staff in all cases by closing the necessary close contact bubbles.”