Richard Sheriff, Executive Headteacher and CEO of Red Kite Learning Trust, said one student is currently at home after testing positive for Covid-19 and around 40 other students are now self-isolating as a precaution.
Those who had any "significant" contact with the pupil have been identified by the school and told to stay at home for 14 days in case they present with any symptoms, in which case they should be tested.
The student who tested positive has not attended the school since before the weekend and is staying at home for the required seven days. They have a sibling at the school who is also currently self-isolating.
Mr Sheriff said: "With more than 2000 pupils in the school it was likely that we would get at least one case and we were prepared for it.
"The headteacher, Mr Renton, followed all the necessary protocols and spoke to Public Health England and North Yorkshire County Council as soon as he got the news, following all of their advice.
"The child is fine, they are self-isolating with their family, and we have good procedures in place which mean we have been able to identify everyone who had any signifcant contact with them and send them home to isolate too. That equates to around 40 students."
Mr Sheriff has thanked parents for their patience and understanding at this difficult time and wants to reassure them the school is still a safe place to be.
He added: "We have had a great start to the year, the children have been so happy to be back and so have the teachers.
"We knew there would be a couple of blips but the good news is we have all the right procedusres in place and this proves that they are effective and work well.
"We are doing everything we can to protect students and their families and to keep this as a safe space and we are very proud of that.
"We have been in touch with all parents individually and I would just like to thank them for their support."
The school, which welcomed back many of its pupils last week for the first time since before the lockdown, is open as normal for those unaffected.
One-way systems, specially-spaced desks keeping students apart and staggered start and finish times have been introduced to help prevent the spread of the virus.
Mr Sheriff is now urging everyone to stick to the rules as much as they can to limit the spread and keep people safe.
He said: "Our measures at school are very thorough but it is so important that people are sticking to the rules and restrictions wherever they go.
"Children spend more time out of school than in it, and we need to make sure we are all doing our bit to stop this virus."