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The COVID-19 pandemic has had profound effects on mental health of children. This study aimed to explore the trajectories of emotional and behavioral problems in children aged 1–6 years over four time points from April 2020 to May 2021 and to identify predictors of these trajectories. This longitudinal study involved four assessments with anonymous online surveys completed by 527 - 888 parents of children aged 1–6 years in Austria, Germany, and Switzerland. Emotional and behavioral problems were measured using the Child Behavior Checklist (CBCL/1.5-5). Sociodemographic data, COVID-19 exposure, child worries, and parental mental health were also assessed. The prevalence of clinically significant behavioral problems ranged from 4.2% to 11.5%, higher than the normative 2%. Latent class growth analyses identified two trajectory classes for anxiety and affective problems: low-symptom and high-symptom classes. For oppositional-defiant problems, three classes emerged: low, medium, and high-symptom classes. The high-symptom classes constituted between 13.1% and 15.6% of the sample, depending on the symptom domain. High symptom trajectories showed little change over time and were significantly predicted by parental mental health (anxiety and depression; OR 1.13–1.21) and child worries (OR 1.19–1.24), with female sex being a predictor for high affective problems (OR 1.90). This study shows that a significant minority of young children experienced elevated emotional and behavioral problems during the first year of the pandemic, primarily influenced by parental mental health and child worries. The identification of a relatively stable high-symptom class points to the need for targeted and timely interventions for those at higher risk. These findings emphasize the importance of supporting parental mental health and addressing children’s worries to mitigate the adverse effects of the pandemic on young children’s mental health.