All children in this age group in England are being offered one dose of the Pfizer-BioNTech Covid jab, which they will receive in schools.
But some schools have already been targeted by anti-vaxx protesters sending letters threatening legal action if they take part.
Geoff Barton, general secretary of the Association of School and College Leaders, said: “Schools deserve huge thanks for all they are doing in hosting coronavirus vaccination sessions for 12 to 15-year-olds, particularly given the speed at which this is all happening and the intense public focus on this programme.
“They again find themselves in the eye of a storm, on this occasion because of the strong views held by some people about this vaccination programme.”
He added: “Those who are opposed to this programme should remember that it is an offer of a vaccination and that pupils, along with their parents or carers, can decide whether or not to take up that offer.
“We would urge groups or individuals not to send letters to schools containing legal threats and not to protest outside schools.
“The role of schools is limited to hosting these sessions and dealing with associated communications, and it is quite wrong to make them the target of opposition.”
It comes after new guidance gives schools advice about how to respond to anti-vaxx protests outside their gates. It clarifies that the School Age Immunisation Service is legally responsible for the delivery of the vaccine, and schools are urged to contact the service to discuss security planning.