Background: Pathogenic bacteria constitute a severe concern in educational settings since regular interaction with many pathogens happens throughout the day. With children mixing daily, this environment makes it easy for illnesses to spread. This paper investigates the application of pharmacoeconomic methods to assess different antimicrobial interventions conducted in educational institutions to reduce exposure to microorganisms and pathogens. The main objective of this study was to directly compare those disinfection interventions in terms of value for money (or cost-effectiveness) and quantify the implications for cost savings and health improvement through their impact on the quality of pathogen destruction. Materials and methods: This study was performed in education facilities in New Zealand. It analyzed the effectiveness of the interventions through pharmacoeconomic analysis approaches—cost-minimization analysis (CMA), cost-benefit analysis (CBA), cost-effectiveness analysis (CEA), and cost-utility analysis (CUA). Results: Prevention of pathogen infection in educational institutions was over 90% when antimicrobial coatings (aqueous solution-based products) were used compared to traditional disinfectants, which was 6.7 quality-adjusted life years (QALY). Higher initial investment brings lower final costs, but also greater health benefits for users of educational institutions. Conclusion: The outcomes obtained with used methods have shown that the effectiveness of antimicrobial coating—aqueous solution-based products compared to traditional cleaners was significantly superior.