Background Meeting physical activity and screen time guidelines has been associated with improved health in children. Research has shown that lifestyle behaviours happen in combination and can be tracked into later life. Thus, a complex approach is needed to identify the effects of physical activity and screen time altogether. This study aims to identify clusters of both behaviours in a cohort of Irish 3-year-old children (n = 8833) and determine the association with sociodemographic characteristics and behaviours at age 5 and 7-8. Methods Data from the "Growing Up in Ireland" study collected between 2010 and 2016 was used in this study. Two-step cluster analysis was used to understand how physical activity and recreational screen time behaviours group together among 3-year-old children. Binary logistic regressions were conducted to examine if cluster placement at age 3 determined physical activity and recreational screen time behaviours at age 5 and 7-8 years, while controlling for gender of child, gender, age and employment status of the primary caregiver. Results Six clusters were identified in 9771 (49.3% female) 3-year-old children with the majority falling into a "High Active & Mixed Screen Time" (23.2%). Those in the "High Active & Mixed Screen Time" cluster at age 3 were more likely to engage in all physical activities reported at age 5 (p < 0.01) and age 7-8 (p < 0.01) when compared to a "Low Active & Screen Time Exceed" cluster. Children categorised in a "Moderate Active & Screen Time Below" and "Moderate Active & Screen Time Exceed" were more likely to engage in the same physical activities at age 5 and 7-8 (p < 0.05 - p < 0.01). However, children in the latter cluster were also more likely (p < 0.05) to play on a computer or tablet device. Conclusions This paper highlights the importance of establishing positive health-related behaviours during early childhood, as this predicts future engagement in health-promoting activities. Regardless of screen time level, being part of a cluster with moderate or high levels of physical activity positively influences a child's future physical activity at age 5 and again at age 7 -8 years. The multiple layers of influence on a child's development should be leveraged to support the adoption of health-enhancing behaviours.