Despite some studies showing seasonal variations in mortality and the transition to renal replacement therapy in patients with end-stage renal disease, detailed evidence is still scarce. We investigated seasonal variations in patients with end-stage renal disease using a large Japanese database for dialysis patients. We compared the fractions of all-cause and cause-specific mortality and the transition to renal replacement therapy among seasons and performed a mixed-effects Poisson regression analysis to compare the mortality among seasons after adjustment for some variables. The initiation of hemodialysis was highest in winter and lowest in summer. Seasonality in the initiation of peritoneal dialysis and transition to kidney transplantation differed from hemodialysis. All-cause mortality was highest in the winter and lowest in the summer. Death from coronary artery disease, heart failure, cerebral hemorrhage, and infectious pneumonia had similar seasonality, but death from cerebral infarction, septicemia, or malignant tumor did not have similar seasonality. In conclusion, the initiation of hemodialysis, all-cause mortality, and mortality from coronary heart disease, heart failure, cerebral hemorrhage, and infectious pneumonia were significantly highest in winter and lowest in summer. However, the initiation of peritoneal dialysis, transition to kidney transplantation, or mortality from cerebral infarction, septicemia, or malignant tumor did not have similar seasonal variations.