Objectives Antimicrobial resistance (AMR) is a severe global health threat, with a disproportionate impact on low-income countries like Somalia. This study aimed to evaluate the effectiveness of the e-Bug educational module in improving knowledge and understanding of AMR among secondary school students in Mogadishu, Somalia, a setting with limited public awareness and a high burden of infectious diseases. Methods A prospective quasi-experimental pre-post study was conducted among 384 Form four (Grade 12) students in Mogadishu. A structured questionnaire assessed knowledge of microbiology, hygiene, and AMR before and after the implementation of the e-Bug educational module. The intervention consisted of standardized, interactive lessons on AMR, hygiene, and infection prevention. Changes in knowledge were analyzed using descriptive statistics, and the McNemar-Bowker test was used to determine the statistical significance of the change in responses from pre-test to post-test. Results Participants were predominantly male (54.2%), with most aged 16-18 years (51.6%). Baseline data revealed strong knowledge of general hygiene, such as handwashing (93.5%), but notable misunderstandings regarding AMR. Notably, 61.5% of students incorrectly believed antibiotics are effective against viral infections like influenza. Following the e-Bug intervention, a statistically significant improvement in overall AMR knowledge was observed (P = 0.003). Post-test results showed enhanced understanding of key AMR concepts, including a 9.6% increase (from 84.4% to 94.0%) in the awareness that antibiotic misuse drives resistance. However, the misconception that antibiotics treat viral infections remained prevalent (58.3%). Conclusions The e-Bug educational module is an effective tool for improving AMR knowledge among secondary school students in Mogadishu. However, the persistence of critical misconceptions, particularly regarding the use of antibiotics for viral illnesses, highlights the need for sustained and reinforced educational efforts. Integrating the e-Bug module into the national curriculum and developing targeted public health campaigns are recommended to address these deep-seated misunderstandings and combat the growing threat of AMR in Somalia.