Renal transplantation is the treatment of choice for end-stage renal disease (ESRD) due to pauci-immune crescentic glomerulonephritis (PICGN). A small subgroup of patients with PICGN are anti-neutrophil cytoplasmic antibody (ANCA) negative. We report a case of a patient with ANCA-negative renal-limited form of PICGN who developed ESRD despite treatment. He underwent live-related renal allograft transplantation after 12 months on haemodialysis. In the eighth post-transplant month, he developed graft dysfunction, which on evaluation turned out to be a graft recurrence of the basic disease in the form of PICGN. He received treatment with methylprednisolone, cyclophosphamide and plasmapheresis. However, his renal functions did not improve and he developed graft loss in the 11th post-transplant month and was started on continuous ambulatory peritoneal dialysis. We report a rare recurrence of renal-limited PICGN in the allograft. Patients with PICGN undergoing renal transplantation should be followed up carefully, and an early biopsy should be performed in the case of graft dysfunction to deal with this potentially graft-threatening complication.