BackgroundChildren’s screen time activity has increased significantly during the pandemic. Extended school closures and heightened parent stress are associated with children’s behavioural difficulties and time spent watching screens. The primary aim of this study was to determine which school and household factors were associated with challenging behaviours in Canadian schoolchildren during the COVID-19 pandemic.MethodsThis longitudinal survey study examined the association amongst screen time, internalizing and externalizing behaviours in school-aged children at two time points over the 2020–2021 academic school year. Parents completed survey measures on their parental involvement, stress levels, and their child’s screen time use as well as their emotional and behavioural difficulties.ResultsChildren’s average daily screen time was 4.40 h (SE= 18.45) at baseline and 3.89 h (SE= 16.70) at 1-year follow up, with no significant change across the school year (p= .316). Increased screen time use was associated with a greater incidence of internalizing behaviours in children (p= .03). Children who spent more time on screens and who were in households with parents reporting higher stress levels had increased internalizing behaviours (p< .001). No association between screen time use and externalizing behaviours was evident; however, parent stress was positively associated with children’s externalizing behaviours (p< .001).ConclusionsChildren’s screen time use has remained high during the pandemic and is associated with anxious and depressive symptoms. Children who spent more time on screens and who were in households with parents reporting higher stress levels had increased internalizing behaviours. Parent stress was positively associated with children’s externalizing behaviours. Targeted family intervention plans focused on reducing parent stress and screen time use may aid in improving children’s mental health during the ongoing pandemic.