Peroxisome biogenesis disorders (PBDs) are a genetically heterogeneous group of metabolic diseases caused by impaired peroxisome assembly and function. PBDs exhibit striking clinical variability, ranging from lethal neonatal forms (e.g., Zellweger spectrum disorders) to milder childhood-onset presentations such as rhizomelic chondrodysplasia punctata. While elevated levels of very-long-chain fatty acids (VLCFAs) remain a key diagnostic feature, the existence of unusual cases with normal plasma VLCFA levels highlight the limitations of relying solely on this biochemical marker for diagnosis. Genetic variations in PEX6, an important peroxisome biogenesis factor, contribute significantly to this phenotypic diversity, with missense variants often associated with less severe disease compared to truncating mutations. Recent studies further implicate dysregulated pexophagy—a targeted autophagic degradation of peroxisomes—in the underlying disease mechanisms. This review underscores the necessity for a multifaceted diagnostic approach that, thorough clinical assessment, detailed biochemical evaluation, and advanced molecular genetic testing, seeks to improve diagnostic accuracy and patient care, particularly in pediatric populations. Advancements in identifying novel biomarkers and targeted therapies offer promise for tailored interventions, underscoring the importance of precision medicine in optimizing outcomes for pediatric PBD patients.