Objectives: Pneumocystis jiroveciii pneumonia (PJP) is still common in the era of universal prophylaxis after kidney transplantation; however, short-term universal prophylaxis has led to delayed onset of PJP beyond 6 months after kidney transplantation. Therefore, we aimed to determine the nationwide status of PJP prophylaxis in Korea and compare the incidence, risk factors, and outcomes of early and late PJP in kidney transplant patients using data from the Korean Organ Transplantation Registry (KOTRY), a nationwide Korean transplant cohort. Methods: We conducted a retrospective analysis using data of 4,839 kidney transplant patients from KOTRY between 2014 and 2018, excluding kidney transplant patients who received multi-organ transplantation or were under 18 years old. Cox regression analysis was performed to determine risk factors for early and late PJP. We also conducted a survey to determine the PJP prophylaxis regimens in 32 KOTRY-participating Korean transplantation centers. Results: A survey showed that 85% and 9% of centers adopted universal PJP prophylaxis and indicated prophylaxis for high-risk patients, respectively. A total of 50 patients developed PJP with an incidence of 4.90 per 1,000 patient-years. Half of the patients developed early PJP within the first 6 months after transplantation, and the other half developed late PJP after 6 months. There were no differences in the rate, duration, or dose of PJP prophylaxis between early and late PJP. Desensitization, higher tacrolimus dose at discharge, and acute rejection were associated with early PJP. In late PJP, old age as well as acute rejection were significant risk factors. Although PJP increased mortality, there was no difference in mortality rates between early and late PJP.  Conclusions: Late PJP is as common and risky as early PJP and requires individualized risk-based prophylaxis, such as prolonged prophylaxis for old patients with a history of rejection.