Pediatric emergency infectious diseases necessitate rapid and accurate etiologic diagnosis to inform timely, life-saving interventions. However, conventional diagnostic approaches are often hindered by prolonged turnaround times and limited capability in detecting diverse pathogens. Oxford Nanopore Technologies (ONT) sequencing, a fourth-generation, real-time genomic platform, offers a transformative solution. With unique features such as ultra-long read lengths, real-time data streaming, and portability, ONT enables comprehensive microbial characterization directly at the point of care, even from low-biomass clinical specimens. This review outlines the fundamental principles of ONT sequencing and recent advances in protocol optimization for challenging pediatric samples. We highlight its groundbreaking applications in acute respiratory, bloodstream, and central nervous system infections, demonstrating its capacity to simultaneously deliver pathogen identification, antimicrobial resistance profiling, and strain typing. Moreover, ONT facilitates novel insights into host-pathogen interactions through integrated genomic and transcriptomic analyzes. We also address current challenges, including bioinformatics complexity and analytical standardization, and propose pathways toward integration within a precision infectious disease framework. Beyond diagnostics, ONT is emerging as a powerful tool to advance infection biology and improve clinical outcomes in children.