Hi user
Sorry to hear that your DS is going through a tough time.
I don't think your only option to remove him from the situation is to remove him from the school.
First, you could speak to both his form tutor and Head of Year and raise your concerns so that they can keep an eye on him.
Second, you could speak openly with him about what is upsetting him and even if he won't volunteer any specifics, you can say that he does seem unhappy and suggest that, if particular people/friends are upsetting him, he try to keep his distance from them. You could give him strategies to do this, as it can be hard at that age to distance yourself from friends. He could, for example, choose to go to the library instead of being in the playground at break. Or go to the canteen or wherever else he is allowed. If the friend tries to follow him, he could say that he would like to be alone/that he has work to get on with/that he's obsessed with reading his book/whatever works for him.
Third, you could encourage other, more positive friendships. Perhaps he could join new or different clubs inside and outside of school which will lead to new friendships. As soon as he knows for himself that this particular friend is causing him misery, he will hopefully choose to avoid the friend. I know this whole situation seems very miserable, and I went through it with my own DS at the same age, but it is all part of growing up. There are nasty people throughout the world and we all have to choose to rise above them, keep our distance from them, and look after ourselves and our own mental health. Some children learn all this without our help, for others, teaching them how to do this is a part of parenting.
Fourth, ensure that he has other things that raise his self-esteem. Make sure he is engaging in activities that make him feel good and through which he can find a sense of achievement; praise him for his good manners, helpfulness, sense of humour, tidy bedroom, anything at all! Tell him what a good judge of character he is and remind him of lovely friends he's had in the past; that might help him to realise that this particular friendship isn't healthy.
My DS did realise that a particular group of boys were not real 'friends' and now keeps his distance from them. The process of distancing himself was quite hard, and it was a rocky couple of months, but he now gets along 'ok' with them, without choosing to spend any more time with them than he has to. Which is perfect. He has developed two other close friendships with supportive, fun boys. I'm sure it will all work out ok for your DS if you continue to be positive and try to create positive experiences for him.
These are all just my thoughts. Also, maybe check what this other boy is putting on social media if they are in touch online. My DS actually chose, for himself, to disconnect from all social media for about three months. It was tough, and he rarely went out/had friends over in that time and we worried that he would never have friends again, but he is now happily back online and in a great, positive circle of friends.
Best of luck to you and your DS. 