The Covid-19 pandemic led to unprecedented school closures globally affecting over 1.6 billion students. In Uganda, all educational institutions were shuttered in March 2020 to curb virus spread. This study examined impacts of prolonged lockdowns and isolation on early pregnancies among school children in rural Kamuli District, Eastern Uganda. A mixed-methods sequential exploratory design combined qualitative interviews with key stakeholders and a household survey. In-depth interviews were conducted with 20 district health and education officials, community leaders, and adolescents. Additionally, a cross-sectional study utilizing multi-stage cluster sampling surveyed 300 young mothers aged 13-19 from 30 villages. Data underwent thematic coding and statistical analysis. Qualitative findings indicated socioeconomic strain related to loss of learning and play exacerbated childhood vulnerability to sexual exploitation. The survey found 22% of respondents reported becoming pregnant during lockdown, tripling district weekly averages. The majority cited parental neglect and seclusion due to school closures as precipitating factors. Pregnant students accounted for 30% dropouts thus far indicating long-term repercussions. Prolonged lockdowns critically threatened developmental needs of adolescents, disproportionately impacting girls. Holistic support integrating sexual health, gender equality and youth empowerment programming remained urgently needed. Strategies bolstering household economic security and remote learning alternatives could have helped curb unintended outcomes of future crises.