Non Attendance at school

Children at 13 are often very protective of their parents and don't want to worry them about things like bullying. So he may be hiding something. Having lots of friends doesn't mean he can't be being bullied. Indeed bullies sometimes target such children because they are jealous.
I think you need to find out if there is a specific part of the school day he can't manage, and if there is contact the school and arrange ways to help him through the difficult time.
Go back to the school and ask that he be given work to do if he stays at home (It's easy enough to e-mail stuff to him on his non-attendance days)
The miracle to me is that any child manages to get through the nightmare of secondary education.

My GS, at around the same age presented the same problem. The head and head of year were just as good as your GS's teachers. He was referred to the school counsellor and developed a good relationship with her. If your GS's school has a counsellor, it would be a good idea to have him referred. Child psychologists are snowed under and he could be grown up before he reached the head of that queue, but if the parents have medical insurance that covers their children, it might be possible to find one.

My GD has had issues with school since they returned after the pandemic .She and her sister help care for their sick mum and she was so scared that being among a lot of people would be a danger to mums health that she just refused to go.
She gets stressed and crys and even the bus trip to school will make her physically sick .Its 20 miles to school so some days she makes it in only to be sent/brought back home
The school has been brilliant ,she gets work for when she cant /wont attempt to go and a councillor who speaks to her every day .Theres a support worker who will drive her in and back whenever she's had enough of what she calls the too peopley place .
If your GS has issues you aren't aware of ask for help from the schools mental health professionals ,they'll work out how best to help him through whatever bothers him about school .They have been a godsend to us,if its any consolation my GD is still doing exceptionally well in her grades ,hopefully you'll get the same support for your GS.Good luck to you all

I agree: I am surprised at the Head of Year's attitude, particularly him citing having missed so much time during the pandemic as an excuse. The boy's mother has checked out the possible causes: illness, anxiety and bullying so it sounds as though her son may simply be lazy, and this will develop into school refusal if allowed to continue unchecked. If his absences are recorded as unauthorised then the school Attendance Officer (whatever the title is now) should be involved.
The boy's father?

It’s always worrying when children refuse school and it’s often a problem exacerbated by frequent absences, because children know they’ve missed learning which may be difficult to catch up.
Perhaps worth your daughter looking at this information on EBSA (Emotionally Based School Avoidance)
www.supportservicesforeducation.co.uk/Page/20029
There’s a big push for schools to look at this especially following the pandemic.
I hope the you find some support for this problem.

Has he actually had a medical work up? There could be something medically wrong. This should be ruled out before assuming it must be psychological.

Parents often think they know their children very well - in my experience that is not always the case. I think his head of year is being rather dismissive. Your GS is happy to have his privilages removed , it is a price he is prepared to pay in order to miss school - that is a worry. Perhaps your daughter could ask him to sit with her then be direct " I know you are unhappy and want you to tell me why that is" If he is anxious about something then he may well be relieved to be given the opportunity to offload. On the other hand he may say nothing , but at least the door is open and he will know that. Either be way there is nothing lost. He may of course just rather be at home than school!! In your daughters situation I would seek professional support if missing school continues. If there is an underlying concern then it can be addressed and not getting to the bottom of it will only serve to make things worse. I wish you all the best.

I think his teacher is very wise and gave good advice. It might help if he could see a councillor or the school psychological service

My DGS, much the age of your DGS has been having similar problems, again he is bright and very sociable. he goes to a fairly 'straight' school that has routines and rules that govern the children, and in this case it is this DGS is struggling with. He keeps forgetting things and is constantly worrying about this.

Thankfully, we think we know what the problem is. Neuro diversity runs in our family. I have dyspraxia and ADHD, DS has dyspraxia and ADD and we now think that DGS has ADHD. Not the extreme kind that has children unable to learn and bouncing off the walls, but one of this syndromes main symptoms, is difficulty with doing or keeping things in order or doing things to a routine.

We have spoken to the school who have referred him for assessment and have eased up in constantly pulling him up for not doing or not following school routines.

Has your daughter asked him what's going on? I think the teacher is reassuring as often young teenagers push against boundaries and attending school is one. It's probably a phase. The feeling of having the house to himself too might be enjoyable. I think she might make it as boring as possible. If she's at work, then enlist you to sit with him at his house or yours. No computer, phone or TV on. It's good she's keeping an eye on it. If it ramps up, tell him she's taking him to the doctor as he's obviously unwell.