© 2019 John Wiley & Sons Ltd Background: Parental incarceration (PI) is associated with adverse developmental outcomes for children affected. However, research in this area often reports conflicting results with few studies following children across time in non-U.S. populations. Additionally, more research is called for using multi-informant perspectives rather than relying on adult reports of child outcomes alone. Methods: This study used data from the first two waves of a nationally representative cohort study of 8,568 children aged 9 years and followed up at age 13 living in the Republic of Ireland (2007¿2012). Propensity score matching was used to match children who had experienced PI by the age of nine to children who had not experienced PI by sociodemographics and experience of other stressful events. Mental health, as measured by self-concept (Piers-Harris II) and externalizing and internalizing difficulties (strength and difficulties questionnaire), was compared across both groups. Results: Fifty of the 8,568 children (weighted percentage 0.9%) reported experiencing PI by the age of nine. These children came from more socially disadvantaged homes and were more likely to have experienced other potentially stressful life events. In comparison to a matched sample of children not affected by PI, children affected by PI reported higher levels of anxiety at age nine. Longitudinal analysis indicated these children affected by PI also reported lower levels of happiness at age 13 with higher levels of emotional difficulties reported by their primary caregiver. Conclusions: Children of incarcerated parents face a greater array of life challenges. PI had an association with child-reported levels of anxiety at age nine. PI also had a medium-term association on caregiver assessments of emotional difficulties of children affected as well child-reported levels of happiness over time.