The pupils, from Heptonstall Junior and Infant School, Hebden Bridge, are all from the reception and nursery classes and are being treated at Calderdale Royal Hospital.
The first was admitted last Friday and today hospital bosses said they were still trying to identify the strain of meningitis. They said one of the children had been sent home yesterday and the other two were stable.
Dozens of worried parents have removed their children from the hill-top school until the strain of meningitis is identified. All classmates of the affected pupils were given antibiotics on Wednesday.
One mum Dorothy Wood, of Colden, has a four-year-old son, Dylan, in the same class as the sick children.
She said the outbreak was being taken very seriously by school staff.
"They have done everything they can to minimise the risk to other children but I think a lot of parents are still panicked," she said.
"My daughter had the worst strain when she was younger and she pulled through but it can kill you.
"My son has been dosed up on antibiotics and I am just praying that he hasn't caught it. It is a really horrible bug to get and can be extremely dangerous."
There are several different types of meningitis.
Viral meningitis is the most common and is almost never life threatening.
Bacterial meningitis which causes inflammation of the brain or septicaemia, severe blood poisoning, is more serious and can be caused by a range of different bacteria. Bacterial meningitis is a life threatening form of the disease and can kill in a matter of hours.
Graham Wardman, director of public health at Calderdale Primary Care Trust, confirmed three children had contracted the infection but that the hospital were still running tests to determine how serious the strain was.
"The children are all currently stable," he said. "But we have advised the school and all the appropriate action has been taken.
"Meningitis does not pass easily from person to person. However, it is always important to be vigilant for the signs and symptoms of meningitis and to seek medical advice if there is any concern."
A spokesman for Calderdale Council said there were no plans to close the school.
But Viv Brearley from the Health Protection Agency, said all measures had been taken to protect the bug from spreading to other staff and pupils.
"In serious cases you can die from meningitis," she said. "So it is obviously being taken extremely seriously.
"We tend to see outbreaks in children and young adults but it can affect anybody."
ellen.widdup@halifaxcourier.co.uk