Kirklees local authority has written to the parents of children at Overthorpe Church of England junior and infant school and Thornhill High School, giving advice and information about the disease which killed a Leeds University student this week and two pupils in a Lincolnshire school last month.
The latest outbreak has affected two boys, aged 16 and 10, and a 10-year-old girl. However, Rob Vincent, Kirklees' chief education officer, said the authority acted swiftly to reassure headteachers and parents there was no cause for alarm.
"Our advice from West Yorkshire Health Authority and experts in this particular field is that the cases are unlikely to be anything more than a coincidence," he said.
Parents were worried, but were accepting the advice and most were continuing to send their children to the schools. Pupils at Overthorpe were given diagnostic swabs and offered antibiotics on Wednesday by health authority staff.
Meningitis outbreaks tend to occur in cycles and peak in winter, a Department of Health spokesman said. "There is little schools could do to prevent this from happening. Staff must look for warning signs."
Young children are particularly vulnerable and it also affects teenagers and the elderly. In the early stages it is similar to 'flu.
There are three strains: viral meningitis, now virtually eliminated since the introduction of the HIB vaccine; bacterial meningitis, which is life-threatening and which struck at City School, Lincoln; and pneumococcal meningitis, which can be treated by vaccine.
Symptoms include: fever, headache and nausea, a stiff neck and rash. The bacteria can only be spread by prolonged personal contact such as kissing.
Staff and pupils at City School were immunised last weekend. "Our investigations point to the outbreak being related to the normal social activities of teenagers and not the school," said Dr Mandy Bretman, acting director of public health medicine.
A 16-year-old girl from Godolphin Latymer School, Hammersmith, west London, is recovering from the disease.