Research has shown that childhood physical activity participation has a positive relationship with markers of wellbeing, such as self-esteem and quality of life, and physical activity participation may serve as protective mechanism against some mental illnesses including depression. The aim of the current study was to examine the relationship between gender, physical activity, screen time, body mass index and wellbeing in Irish school children (N = 705; mean age: 8.74 ± 0.52 years) from social disadvantage. In Northern Ireland, schools included in the 2010 Multiple Deprivation Measure (NIMDM) were invited to participate. Schools included for participation in the Republic of Ireland were from the Delivering Equality of Opportunity in Schools (DEIS) index. Data gathered included accelerometry (physical activity), self-report (screen time and wellbeing), and anthropometric measurements. Physical activity was objectively measured during eight consecutive days using Actigraph GT1M and GT3X devices, using stringent accelerometer protocol. Screen time activities were derived using questions adapted from the Health Promotion Agencies National Children’s Survey in Northern Ireland. The KIDSCREEN-27 is a health-related quality of life measurement, and this tool was used by participants to self-report their health and wellbeing. Results suggest that boys accumulated more minutes of daily screen time than girls, however, boys were more physically active when compared to girls. Wellbeing scores for gender showed inverse associations with daily screen time. Standard multiple regression revealed that gender, physical activity, screen time and body mass index (combined) explained little variance in the prediction of wellbeing. Results indicate the importance of gender-based considerations for physical activity and screen time with children from social disadvantage. The inverse relationship found between overall screen time and wellbeing will help guide future healthy lifestyle interventions for Irish children of low-income communities.