Walking school buses and bicycle trains are highly favored mobility concepts to promote children’s interest and safety in active travel to/from school, reduce private vehicle dependency and pollution in cities, and promote healthy lifestyles. So far, these supervised and environmentally-friendly modes of transport have been implemented in the Global North. However, the limited research on in-depth algorithms, modeling, mathematical optimization, and policy frameworks for these cleaner and sustainable transport modes is slowing widespread implementation, particularly in the Global South. Based on 49 selected papers, this systematic review elucidates the benefits, implementation challenges, optimization approaches, methodological gaps, and policies toward cleaner production of these transport modes. Reviewers collected relevant papers from the Web of Science, Scopus, Transport Research International Documentation, PubMed, and WorldCat. The results showed that comparatively, there is more research on walking school buses than bicycle trains, and gender-parity and disability research dimensions are non-existent. Methodologically, placement, scheduling, and routing optimization studies require improvement. Additionally, extensive consultations are necessary to formulate standardized guidelines and upgrade infrastructures to stimulate global implementation and adoption. This study explains knowledge gaps and policy ideas for the practical implementation and holistic development of these clean transport modes for schoolchildren.