To manage the expected high number of vehicles heading to Budmouth Academy over the weekend temporary traffic routes have been put in place, with drivers being diverted via an industrial estate.
The precautionary medical measures will be offered in stages over the coming days to all those in school years 7 to 13 who study or live in the Weymouth, Portland and Chickerell areas.
Anyone not in full-time education who would be in one of those year groups will also be able to have a single dose of antibiotics and the vaccine.
Young people aged under 16 attending the clinic should be accompanied by a parent or guardian who is able to provide consent.
The UKHSA said all those have already taken the preventative antibiotic which gives provided the most effective short-term protection will also be offered a MenB vaccination.
It said more information on the vaccination schedule would be provided in due course.
Information about the signs and symptoms of meningitis have been shared with students and parents.
The Dorset cases have been confirmed as meningitis B (MenB) and are the same sub-strain type, but a different sub-strain, to the one detected recently in Kent.
They are not linked to the deadly Kent outbreak, the health agency said.
All three Weymouth students are said to be recovering well.