The study, commissioned by The Meningitis Trust, looked at the effects of meningococcal group B disease (MenB), the UK's most common type of bacterial meningitis.
Medics at University College London concluded that one in three children who are treated for the disease will go on to have after-affects which could include mental health issues, problems, learning difficulties and epilepsy.
They also found that one in five youngsters will be left with anxiety or behavioural disorders, and will be five times more likely to have speech and communication problems, as well as an increased risk of amputation.
The researchers further found meningitis had an effect on kids' long and short-term memory, and left some little ones with a borderline low IQ.
There was also a five-fold increased in the likelihood of a significant hearing impairment, with 2.4% of children who survived a bout of the illness having bilateral hearing loss which required a cochlear implant.
The chief executive of the Meningitis Trust, Sue Davie, told the Press Association: "The hidden, yet devastating after-effects of meningitis can often be dismissed.
"We hope that the new findings will encourage education and health professionals to recognise these, as well as the noticeable physical after effects of meningitis, and push for children to receive the support they need and deserve.
"In addition, we hope that parents will feel more empowered by these findings. They need to be confident when advising professionals that their child might be suffering from the after effects of meningitis in order to change perceptions, and ensure meningitis is fully investigated as a possible cause."
The research - The Meningococcal Outcomes Study in Adolescents and In Children - studied over 570 children in England over a three-year period.
About 3,400 new cases of bacterial meningitis are diagnosed in the UK each year, and half of the cases are in children. Infants under five, youngster aged 15 to 24 and adults over 55 are most at risk of the illness, the charity say.