BackgroundPneumocystis jirovecii pneumonia (PJP) is a common and troublesome complication of kidney transplantation. In the era of prophylaxis, the peak incidence of PJP after kidney transplantation and specific characteristics of late‐onset PJP have always been debated.MethodsWe performed a retrospective study by analysing the data of post‐transplantation pneumonia in adult kidney transplantation recipients between March 2014 and December 2021 in The Affiliated First Hospital of University of Science and Technology of China (USTC). A total of 361 patients were included and divided into early‐onset PJP, late‐onset PJP and non‐PJP groups. The characteristics of each group and related risk factors for the late‐onset patients were investigated.ResultsSome patients developed PJP 9 months later with a second higher occurrence between month 10 and 15 after transplantation. Compared with non‐PJP, ABO‐incompatible and cytomegalovirus (CMV) viremia were significantly associated with late onset of PJP in multivariate analysis. The use of tacrolimus, CMV viremia, elevated CD8(+) T cell percent and hypoalbuminemia were risk factors for late PJP. Receiver operating characteristic curve analysis demonstrated that a combination of those factors could increase the sensitivity of prediction remarkably, with an area under the curve of 0.82, a sensitivity of 80% and a specificity of 83%.ConclusionsPJP could occur months after kidney transplantation. ABO‐incompatible transplant recipients are at high risk of PJP. In the later stages of transplantation, CMV viremia, T lymphocyte subsets percentage and serum albumin levels should be monitored in patients using tacrolimus.