Several studies investigated short-term risks of children born from unintended pregnancies, however evidence about long-term risks is lacking. We aimed to examine whether children born from unintended pregnancies experience psychosocial problems up into adolescence. This study is based on the longitudinal birth cohort study ‘Amsterdam Born Children and their Development’ (n = 7784). Unintended pregnancy was measured as a multidimensional construct, based on self-reports on the extent of pregnancy mistiming (‘This pregnancy happened too soon’), unwantedness (‘I did not want to be pregnant (anymore)’) and unhappiness (‘I am happy to be pregnant’; recoded). Further, children's psychosocial problems were measured with the Strengths and Difficulties Questionnaire, at 5–6, 11–12 and 15–16 years old. Multiple over-time associations between unintended pregnancy and children's psychosocial problems were analysed using Structural Equation Modelling, while controlling for confounders. Results showed that pregnancy mistiming was a significant predictor of internalizing (β = 0.10, p < 0.001) and externalizing problems (β = 0.07, p = 0.006) and unwanted pregnancy of internalizing problems (β = 0.13, p < 0.001) at 5–6 years. These associations were substantially mediated by maternal mental health and poorer maternal bonding. Associations were no longer present at 11–12 and 15–16 years. Thus, we conclude that children born from unintended pregnancies experience more psychosocial problems at 5–6 years, but no longer at 11–12 and 15–16 years. Unintended pregnancies often coincide with maternal mental health problems and socioeconomic factors. Most importantly, the associations between unintended pregnancy and children's psychosocial problems are influenced by maternal mental health and poorer bonding. Therefore it is important to improve maternal mental health and bonding for the benefit of both mother and child, rather than on the isolated effect of unintended pregnancy per se.