The main concern regarding mercury exposure is the adverse health effect on the developing nervous system. The objective of this cross-sectional study was to determine hair mercury levels and their association with socio-demographic characteristics, complaints about mercury poisoning symptoms and the fish consumption pattern among children in Malaysia. A cross-sectional study was conducted among 215 school children aged 11 years old. Hair was collected from the children and the total mercury was analyzed using oxygen combustion-gold amalgamation atomic absorption spectrophotometry. Anthropometric data, a fish consumption questionnaire and mercury poisoning symptoms were collected during a personal interview. The mean hair mercury level among primary school children was 0.63 ± 0.59 µg/g with the geometric mean of 0.47 µg/g. A total of 14% of respondents had hair mercury levels above 1 µg/g. A multiple binary logistic regression analysis outlined that fish consumption of at least one meal per week increased the likelihood of having a high mercury level (odds ratio (OR) 3.7, 95% confidence interval (CI) 1.3-10.4). This study confirms the existence of a mercury burden among Malaysian children and the level is high compared to other regional studies. This study provides important baseline data regarding the mercury level among children in Malaysia.