The rising prevalence of mental health disorders among children is a serious concern. Young children who exhibit early warning signs of mental health issues are more likely to develop symptoms in the same or overlapping regions years later. The research aimed to identify emotional and behavioural problems and associated factors in Malaysian preschools. A sample of young children aged 4–6 years from public and private preschools was chosen using a multistage random sampling method. Data were collected from 18 preschools via a parent survey using the Strengths and Difficulties Questionnaire (SDQ). The sample involved 557 children in the SDQ assessment (92%). The overall estimated prevalence of emotional and behavioural problems was 8.4%. Peer problems were the most prevalent attribute, with a percentage of 19.7%. Conduct problems were found in 5.2%, hyperactivity problems in 5.6%, prosocial behaviours in 13.5%, and emotional problems in 6.8%. Girls showed a significant increase in behavioural and emotional problems compared to boys. Having one parent working, having more than two siblings, and having a single-parent family were associated with emotional and behavioural problems. The prevalence of emotional and behavioural problems in Malaysian children was relatively low compared to data from previous studies and other Asian countries but consistent with European studies. Measuring mental health disparities in young children helps stakeholders launch local early intervention programmes.