Pneumocystis pneumonia (PCP) incidence was decreased in renal transplant thanks to prophylaxis, recommended during the first months after transplantation. However, many late PCP cases are observed after the first 6 months and recommendations to maintain or reintroduce prophylaxis are lacking. The objective of the study was to identify risk factors to guide the individual prescription of prophylaxis, 6 months after transplantation. Thirty-three late PCP cases were identified between 1995 and 2012 in Lille Hospital, France, and were compared to 72 randomized controls transplant recipients. In univariate analysis, age of donor (>48 years), retransplantation, a decrease glomerular filtration rate (≤45 mL/min), induction therapy mediated by anti-thymocyte globulin (ATG), steroid maintenance, high calcineurin inhibitors (CNI) doses (tacrolimus ≥0.5 mg/kg/day and cyclosporine ≥2.1 mg/kg/day), and cytomegalovirus (CMV) infection were significantly associated with PCP. In multivariate analysis, ATG (hazard ratio [HR]: 2.4 [1.1-5.4]), steroid therapy (HR: 3.1 [1.20-7.84], CNI (HR: 2.9 [1.28-6.38], and CMV (HR: 6.1 [2.74-16.33] remained associated with late PCP. In conclusion, we confirm that intensive immunosuppressive regimen and CMV infection are critical risk factors for late PCP and should be taken into account to decide on maintenance or reintroduction of a prophylactic treatment.