Despite the lack of evidence that suggests hemodiafiltration (HDF) offers a better survival outcome than standard hemodialysis (HD), the number of patients initiating HDF in Japan continues to rise. This study examined the temporal change in the number of HDF incidents, evaluated factors associated with all-cause mortality, and compared the mortality risk and survival time of patient on HDF with patients receiving standard HD in three sets of 2-year cohorts. The primary analyses included the insurance claims data of 460 HDF patients and propensity score-matched 903 standard HD patients who initiated dialysis therapy between April 1, 2012 and March 31, 2018. Patient follow-up was censored at the time of death or the end of the 2-year study period. The influence of comorbidities on all-cause mortality was investigated, and the survival outcomes between HDF and standard HD patient groups throughout cohorts were compared. The number of HDF patients was increasing throughout cohorts, but the proportions of mortality cases across cohorts slowly decreased. Dementia status increases the mortality risk of patients regardless of dialysis modality. The mortality risk among HDF patients with dementia was more significant than HD patients. Adjusting for all covariates, we observed that HDF patients had a reduced mortality risk and longer survival time than patients on standard HD. This study supports the notion that HDF reduces all-cause mortality compared with standard HD in an incident dialysis population in Fukuoka Prefecture, Japan.