In many Malaysian urban settings, particularly in planned cities like Putrajaya, the daily school commute presents ongoing challenges related to safety, accessibility, and environmental comfort. Rising concerns over child pedestrian safety, traffic congestion during school and rush hours, and the lack of climate-responsive infrastructure highlight the urgent need to rethink the physical environment surrounding schools. These factors contribute to unsafe, uncomfortable, and unsustainable journeys, especially for students who walk, cycle, or use public transport. This research explores how architectural and urban design interventions can improve the safety, comfort, and sustainability of school commute environments for primary and secondary students in Putrajaya. Using a design-based research methodology, the study followed a three-phase process: analysis, assessment, and proposal. The analysis phase involved site observations, stakeholder engagement through surveys with students and parents, and spatial analysis within a 1000–1500-meter radius of selected schools. Observations focused on pedestrian flows, drop-off and pick-up zones, sidewalk conditions, shade availability, and traffic behavior during peak hours. The research also reviewed national and international precedents such as Safe Routes to School (SRTS) and urban traffic-calming strategies. Findings from the analysis led to practical and locally relevant design solutions aimed at creating safer, more sustainable, and comfortable school commutes. The proposal phase recommended architectural interventions including shaded walkways, protected pedestrian crossings, climate-responsive waiting shelters, smart-route cycling lanes, and pedestrian-priority zones. Innovative building materials and low-carbon design strategies were also explored to minimize environmental impact. By focusing on small-scale yet impactful architectural solutions, this research contributes to urban design for education by demonstrating how thoughtful spatial planning can enhance the daily commuting experience of school students in Malaysia. The holistic strategy aims to foster healthier habits, reduce vehicle dependency, and align with global sustainability goals.