Post-infectious glomerulonephritis (PIGN) and atypical hemolytic uremic syndrome (aHUS) can overlap due to alternative complement pathway dysregulation. We report a 4-year-old boy with edema, hypertension, hematuria, and reduced urine output. Laboratory findings included hemoglobin of 11.5 g/dL, platelets of 350 × 109/L, protein/creatinine ratio of 0.6 g/mmol, serum creatinine of 125 μmol/L, C3 of 0.3 g/L, and biopsy-confirmed PIGN. Despite supportive care, corticosteroids, and mycophenolate mofetil, kidney function remained impaired. Ten weeks later, the patient developed thrombotic microangiopathy (TMA) with hemoglobin of 6.5 g/dL, platelet count of 90 × 109/L, and creatinine of 180 μmol/L. Eculizumab was initiated promptly, resulting in rapid hematologic normalization and kidney recovery. Genetic testing revealed mutations in CFHR1/CFHR3 and CD46, confirming susceptibility to complement-mediated aHUS. This case shows that PIGN may trigger aHUS in genetically predisposed children and underscores the need for early recognition and prompt complement inhibition to prevent kidney injury and achieve remission.