Background Citrate dialysate (CD) has been used successfully in conventional hemodialysis and continuous renal replacement therapy but has never been compared between pre- and post-dilution online hemodiafiltration (oL-HDF). Therefore, we investigated the efficacy, metabolic changes, and quality of life of citrate anticoagulation for oL-HDF in the maintenance of hemodialysis patients in both modes. Method Eight dialysis patients were treated with CD for 4 weeks in each phase. The visual clotting scores were investigated as the primary endpoints. The adequacy of dialysis, laboratory parameters, and quality of life were measured as secondary objectives. Results The mean clotting scores in the pre-dilution mode were significantly lower than in the post-dilution and all phases except in the heparin-free phase (P < 0.001 in baseline phase, P = 0.001 in phase 1, and P = 0.023 in phase 2). The quality of life related to physical in the post-dilution mode was significantly higher than in the pre-dilution mode in baseline and phase 1 (P = 0.014 and 0.004 at baseline and phase 1, respectively).The metabolic changes were not different in both modes. Conclusion Citrate dialysate allows decrease or discontinuation of anticoagulation in both the pre- and post-dilution mode of oL-HDF without significant side effects.