The main objective of this study is to thoroughly evaluate the diversity and sources of heavy metals in the school environment. Specifically, this study examines the presence of heavy metals in the dust found and collected from 24 schools in Vilnius. Employing hierarchical cluster analysis, principal component analysis, and positive matrix factorization, we identified combustion-related activities as primary contributors to elevated metal concentrations, notably zinc, scandium, and copper, with PM2.5/PM10 ratios indicating a combustion source. They reveal significant differences in the levels of elements such as arsenic (4.55–69.96 mg/kg), copper (51.28–395.37 mg/kg), zinc, and lead, which are affected by both local environmental factors and human activities. Elevated pollution levels were found in certain school environments, indicating environmental degradation. Pollution assessment and specific element pairings’ strong positive correlations suggested shared origins or deposition processes. While this study primarily assesses non-carcinogenic risks to children based on a health risk assessment model, it acknowledges the well-documented carcinogenic potential of substances such as lead and arsenic. The research emphasizes the immediate necessity for efficient pollution management in educational environments, as indicated by the elevated hazard index for substances such as lead and arsenic, which present non-carcinogenic risks to children. This research offers important insights into the composition and origins of dust pollution in schools. It also promotes the need for broader geographic sampling and prolonged data collection to improve our understanding of pollution sources, alongside advocating for actionable strategies such as environmental management and policy reforms to effectively reduce exposure risks in educational settings. Furthermore, it aims to develop specific strategies to safeguard the health of students in Vilnius and similar urban areas.