<p>This study explores the critical roles of Operation and Maintenance (O&amp;M) in influencing sanitation service levels, as outlined by the Joint Monitoring Program (JMP), in schools across Kampala City. In consideration of access, technology, and condition of sanitation facilities, the JMP classifies sanitation services in schools as basic, limited and no service levels. A cross-sectional study approach and systematic random sampling techniques were used to collect data from 274 schools (selected from 852) using checklists and questionnaires. Results show that 62% and 38% of the schools are operating at limited and basic sanitation service levels respectively. No school was at the "no service" level. Binary logistic regression identified toilet technology, flushing method, cleanliness, and special sanitation budgets as significant O&amp;M factors (<i>P</i> &lt; 0.005). The logistic regression model predicted sanitation levels with 67% accuracy (Chi-Square = 52.251, <i>P</i> &lt; 0.001, Cox and Snell R² = 0.18, Nagelkerke R² = 0.245). Results indicate that schools with waterborne toilets are less likely to operate at limited-service levels compared to those with pit latrines (Odds Ratio (OR) = 0.272, <i>P</i>-value = 0.018). Schools that maintained clean toilets and had dedicated sanitation budgets were more likely to achieve basic sanitation service levels, with odds ratios of 2.109 (<i>P</i>-value = 0.012) and 3.603 (<i>P</i>-value = 0.001), respectively. Implementation of privacy promoting activities have a gain index of 135% which is potentially enough to improve basic sanitation coverage from 38 to 75% of schools in Kampala City. These findings emphasize the importance of improved sanitation technologies, proper maintenance practices, and financial investment all aimed at sustaining improved sanitation service provision. This study provides empirical evidence on factors influencing service levels in Kampala City schools.</p>