First, drop him off, make like you’re leaving then double back to Reception and insist on an appointment with the SENCO and Head of Year. It probably won’t be the same day, that’s fine, just get an appointment. The point is make sure it’s both of them or you’ll get bounced about.
Most secondary schools have a pastoral support team, the SENCO and HOY need to get them on board and working with your son. If you are really lucky the school may also have a professional counselling program. Meeting with them will enable them to try and unpick what factors about school your son is most worried about. They may also have a peer mentoring scheme where they can buddy him up with kids that have the empathy to help him a bit.
If you follow this route and the school stonewall you, then you have to follow the complaints procedure, in the first instance this will be the HT or DHT, then the Governors who will also have a dedicated SEN governor.
Your son doesn’t need to know you’re doing any of this, but you have to put your shoulder into it OP now. I hate to say it, but at least he’s going to school at the moment. In a few months hormones are going to boot in and matters will get worse.
Many posters are telling you their children are like your son. They are also a great source of comfort. They are also telling you to act, and as much as we all can empathise you either have to do that or you are going to have a 6ft tall school refuser and you really will be in the shitter.