Background: The coronavirus disease – 2019 (COVID-19) pandemic has caused devastating effects across all sectors. The closure of schools negatively affected school going children globally. The present study sought to assess the effect of the ongoing COVID-19 pandemic and measures put in place to curb its spread on the psychosocial wellbeing of school going children in Bududa District, in Uganda. Methods: This was a cross-sectional study in which randomly enrolled school-going children from three conveniently selected sub-counties, Bukalasi, Bushiyi, and Bushika, in Bududa District, Uganda. Pretested standardised semi-structured questionnaires were used to collect data on the impact of COVID-19 pandemic on education and psychosocial status of the participants. Results: A total of 210 participants were studied. Of this, 122 (53.3%) were male, 203 (96.7%) lived in rural settings, and 155 (73.8%) were staying with both parents. The median age of the participants was 12 (interquartile range: 9 -15) years. One hundred ninety one (90.9%) participants were in primary school. Overall, 154 (73.3%) were worried about not going back to school during the lock down, however, 109 (51.9%) were able to return to school after the easing of the lockdown. Eighty-five (40.5%) participants received reading material at home during lockdown with 64 (30.5%) of the participants accessing teachings through radio. Of the 210 participants, 174 (82.9%) felt worried about the future, 172 (81.9%) felt like they were going to die during lockdown, 141 (67.1%) felt lonely at times, and 129 (61.4%) felt sad or low sometimes during the COVID-19 pandemic. A quarter (54) of 210 participants faced abuse of which 42 (77.8%) faced physical abuse from parents. Of 31 participants who sought help, 19 (61.3%) went to their parents with none getting help from non-governmental organisations. Fifty (23.8%) participants were engaged in work; 33 (66%) were paid, 4 (8%) were forced to work, and 22 (44%) faced physical challenges at their jobs.Conclusion: There was a substantial impact of the COVID-19 pandemic on the education and psychosocial wellbeing of school-going children in Bududa District. A comprehensive child psychological support service should be scaled up to provide support to school going children in vulnerable communities.