Pneumocystis pneumonia (PCP) has evolved into a late-onset opportunistic infection in the era of prophylaxis, necessitating the definition of reasons for prolonged prophylaxis. As a result, researchers wanted to determine the risk factors for late-onset PCP. The other purpose was to see how the infection affected transplant and patient survival. They matched 1 case to 1–2 controls from the same center based on the transplant date and kind of induction treatment in a French case-control study in Bordeaux and Toulouse. A total of 74 cases and 134 controls were included in the study. PCP occurred 3 years after transplantation on average. On the day of infection and annually for the next 4 years, the total lymphocyte count and CD4+ and CD8+ T-lymphocyte values were lower in the patients than in their matched controls. The absolute lymphocyte count 1 year before Pneumocystis, mTOR inhibitors used as maintenance immunosuppressive medications, and the injection of corticosteroid boluses used in acute rejection were the covariables that were independently related with PCP. The strongest predictor of infection incidence was a total lymphocyte count threshold of 1000/L. PCP was linked to a significant rate of transplant failure and patient death (30% and 17% respectively, 3 years after PCP). Pneumocystis pneumonia has life-threatening implications in kidney transplant recipients; a targeted prophylactic based on basic criteria like chronic lymphopenia and/or a history of corticosteroid boluses could be effective in preventing life-threatening complications.