Studying trends in mental health morbidity will guide the planning of future interventions for mental and public health services. To assess the trends in mental health problems among children and adolescents aged 5 through 15 years in Malaysia from 1996 to 2011, data from the children's mental health component of three population-based surveys was analysed using a two-stage stratified sampling design. Mental health problems were assessed using the Reporting Questionnaire for Children. The prevalence of mental health problems among children and adolescents aged 5 through 15 years showed an increasing trend from 13.0% (95% Confidence Interval [CI]: 11.5-14.6) in 1996 to 19.4% (95% CI: 18.5-20.3) in 2006 and 20.0% (95% CI: 18.8-21.3) in 2011. In 2011, male children and adolescents and those who were in less affluent families were significantly associated with mental health problems. The findings indicate that even though mental health problems among children and adolescents in Malaysia are increasing, the rate of increase has decreased in the past five years. Socially and economically disadvantaged groups were most vulnerable to mental health problems.