The geriatric nutritional risk index (GNRI) and modified creatinine index (mCI) are surrogate markers of protein-energy wasting in patients receiving hemodialysis. We aimed to examine whether a combined evaluation of these indices improved mortality prediction in this population. We retrospectively investigated 263 hemodialysis patients divided into two groups, using 91.2 and 20.16 mg/kg/day as cut-off values of GNRI and mCI, respectively. The resultant four groups were reshuffled into four subgroups defined using combinations of cut-off values of both indices and were followed up. During the follow-up period (median: 3.1 years), 103 patients died (46/103, cardiovascular causes). Lower GNRI and lower mCI were independently associated with all-cause mortality (adjusted hazard ratio (aHR) 4.96, 95% confidence intervals (CI) 3.10–7.94, and aHR 1.92, 95% CI 1.22–3.02, respectively). The aHR value for the lower GNRI and lower mCI group vs. the higher GNRI and higher mCI group was 7.95 (95% CI 4.38–14.43). Further, the addition of GNRI and mCI to the baseline risk assessment model significantly improved the C-index of all-cause mortality (0.801 to 0.835, p = 0.025). The simultaneous evaluation of GNRI and mCI could be clinically useful to stratify the risk of mortality and to improve the predictability of mortality in patients on hemodialysis.