PurposeAssociations between prenatal earthquake exposure and children’s mental health remain unclear. Moreover, there is a paucity of research using quasi-experimental statistical techniques to diminish potential selection bias. Thus, this study aimed to explore the impact of prenatal exposure to the Chilean earthquake of 2010 on children’s behavioural and emotional problems between 1½ and 3 years old using propensity score matching.MethodsParticipants included 1549 families from theEncuesta Longitudinal de la Primera Infanciacohort in Chile. Maternal reports using the Child Behaviour Checklist (CBCL) were used to assess behavioural and emotional problems between 1½ and 3 years old. Information on prenatal earthquake exposure was collected via maternal report. The Kernel matching estimator was used to compare the average treatment effects of children who were exposed to the earthquake compared to those who were not.ResultsFive of the seven CBCL outcomes were statistically significant after matching and adjustment for multiple testing, suggesting greater difficulties for exposed children which included emotional reactivity, anxious/depressed, sleep problems, attention problems, and aggression (mean difference of 0.69, 0.87, 0.73, 0.85, 3.51, respectively). The magnitude of the effect was small to medium.ConclusionFindings contribute to the potential causal inferences between prenatal earthquake exposure and increased behavioural and emotional problems in early childhood. Results suggest that in utero experiences may have long-term consequences for infants’ well-being, supporting the need for specific interventions in pregnancy after natural disasters.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00127-023-02433-z.