This paper examines the vulnerability of school-aged children during their daily commute as an underexplored aspect of soft target protection. The scientific objective is to analyse the current state of school transportation security in Slovakia, identify key vulnerabilities, and propose targeted organisational, procedural, and technical measures to enhance resilience. The research applies a tailored vulnerability assessment framework based on Crime Prevention Through Environmental Design (CPTED) principles and the EN 31000 risk management standard, integrating findings from national security policy and expert forums. Results indicate that current measures are fragmented, reactive, and lack a unified national methodology. The proposed solution outlines a multi-layered security approach combining improved infrastructure design, staff training, intelligent monitoring technologies, and standardised procedures, with potential applicability to other public transport environments. This article addresses the vulnerability of school-aged children during their daily commute to and from educational institutions, highlighting this overlooked phase as a critical component of soft target protection. Despite the growing number of attacks on soft targets globally—including schools, transportation hubs, and public spaces—the transportation of children remains insufficiently considered in national security frameworks. In Slovakia, approximately 175,000 students use public transportation daily, yet security measures at railway and bus stations, as well as in vehicles, are limited or reactive.