IntroductionThe COVID-19 pandemic has impacted the mental health (MH) of children, adolescents and parents. Whereas youth with MH disorders and neurodevelopmental disorders (NDD) may be at higher risk for exacerbations in emotional and behavioural distress, children and adolescents without pre-existing MH disorders or NDD may also experience MH deterioration due to increases in stress, changes in health behaviours, loss of activities/school closures or loss of resources. Little is known about the impact of the COVID-19 emergency measures (EMs) on children’s MH over the course of the pandemic.Methods and analysisLongitudinal study of four well-established, pre-existing cohorts in Ontario (two recruited in clinical settings, two recruited in community settings). Primary outcomes include the impact of EMs on six MH domains: depression, anxiety, irritability, inattention, hyperactivity and obsessive–compulsive behaviours. Risk and protective factors related to youth MH profiles and trajectories will be identified. In addition, the effects of school mitigation strategies, changes in MH services and family factors (ie, parental MH, economic deprivation and family functioning) on children’s MH will be examined. Data will be collected via repeated online survey measures selected to ensure reliability and validity for the proposed populations and distributed through the pandemic periods.Ethics and disseminationThe study was approved by institutional research ethics boards at participating research sites. Results will be disseminated through a robust knowledge translation partnership with key knowledge users. Materials to inform public awareness will be co-developed with educators, public health, and MH and health service providers. Connections with professional associations and MH advocacy groups will be leveraged to support youth MH policy in relation to EMs. Findings will further be shared through conference presentations, peer-reviewed journals and open-access publications.