Background: There are substantial age-related changes in emotional and behavioural problems over childhood. In order to establish the impact of the Covid-19 pandemic on child emotional and behavioural problems, longitudinal designs which take into account age-related trends are needed. This study examined trajectories of children's emotional and behavioural difficulties both before and during the pandemic in a prospective birth cohort. Methods: Data were from 708 children from the third generation of a birth cohort study; the Avon Longitudinal Study of Parents and Children in England. The study population comprised of 708 children (median age at COVID data collection was 2.75 years [interquartile range 0.8, 4.4]) whose parents provided pre-pandemic surveys and a survey between 26 May and 5 July 2020. Multi-level mixed effects models with random intercepts and slopes examined whether children's trajectories of emotional and behavioural difficulties during the pandemic differ from those expected pre-pandemic. Results: Children's emotional and behavioural difficulties trajectories pre-pandemic increased during infancy peaking around the age of 2 and then declined throughout the rest of childhood. Pre-pandemic, decline in difficulties scores after age 2 was 0.6 points per month; but reduced by 35% during the pandemic. This slower decline in scores translated to older children having difficulty scores higher than would be expected, during the pandemic. By age 8.5, there is a 9.5-point difference in pre- and during-pandemic scores (95% CI: 4.5–14.5). This represents an average 48% increase from scores expected at this age (pre-pandemic mean score = 20; 95% CI: [15–25]). Results remained similar although somewhat attenuated after adjusting for parental anxiety. Conclusion: The COVID-19 pandemic may be associated with greater persistence of emotional and behavioural difficulties after the age of 2 years.