Background: Bats provide essential ecological services, including pollination, seed dispersal, and insect control. However, misconceptions regarding their association with infectious diseases have contributed to negative perceptions, particularly following the COVID-19 pandemic. Objectives: This study assessed the knowledge and practices of secondary school students and teachers regarding bat ecology, population dynamics, and potential infectious diseases in selected secondary schools in Agusan del Sur, Caraga Region, Philippines. Methods: A descriptive survey research design was employed using a validated semi-structured questionnaire. Participants included randomly selected seventh-twelve Grade students enrolled during School Year 2022-2023 and secondary school teachers. The instrument underwent pilot testing to establish its reliability. Data were analyzed using descriptive statistics, while the t-test was used to determine significant differences in knowledge and practices between students and teachers. Results: Students agreed with 13 of the 16 statements on bat biology, ecology, and ecological services, with an overall mean score of 2.70 ± 0.30, whereas teachers agreed with nine statements, with an overall mean score of 2.51 ± 0.28. The findings revealed knowledge gaps and misconceptions regarding bats and bat-associated infectious diseases among both groups. Conclusion: Educational programs promoting evidence-based information on bat ecology, conservation, and zoonotic diseases are recommended to improve knowledge, encourage positive practices, support biodiversity conservation, and enhance public health awareness.