Cystinosis is a rare autosomal recessive lysosomal storage disorder with an incidence of approximately 1 in 100,000 to 200,000 live births. It is the most common cause of inherited pediatric Fanconi syndrome (FS). Here, we describe the cases of two infants from unrelated families who presented with polyuria and features of proximal renal tubular dysfunction. Although no corneal cystine deposition was observed at presentation, clinical suspicion and genetic analysis confirmed the diagnosis of nephropathic cystinosis. Both patients carried the same pathogenic variant in the CTNS gene, suggesting that it is a hotspot in this region. These patients were managed with oral cysteamine therapy, cysteamine eye drops, and supportive therapy for FS and are currently doing well. Genetic diagnosis plays a crucial role in the early detection of cystinosis, facilitating timely initiation of cysteamine therapy, and should be considered in infants with FS.