Mortality at an early stage after kidney transplantation is a catastrophic event. Treatment-related mortality (TRM) within 1 or 3 months after kidney transplantation has been seldom reported. We designed a retrospective observational cohort study using a national population-based database, which included information about all kidney recipients between 2003 and 2016. A total of 16,073 patients who underwent kidney transplantation were included. The mortality rates 1 month (early TRM) and 3 months (TRM) after transplantation were 0.5% (n = 74) and 1.0% (n = 160), respectively. Based on a multivariate analysis, older age (hazard ratio [HR] = 1.06; P < 0.001), coronary artery disease (HR = 3.02; P = 0.002), and hemodialysis compared with pre-emptive kidney transplantation (HR = 2.53; P = 0.046) were the risk factors for early TRM. Older age (HR = 1.07; P < 0.001), coronary artery disease (HR = 2.88; P < 0.001), and hemodialysis (HR = 2.35; P = 0.004) were the common independent risk factors for TRM. In contrast, cardiac arrhythmia (HR = 1.98; P = 0.027) was associated only with early TRM, and fungal infection (HR = 2.61; P < 0.001), and epoch of transplantation (HR = 0.34; P < 0.001) were the factors associated with only TRM. The identified risk factors should be considered in patient counselling, selection, and management to prevent TRM.