Background: In patients on maintenance dialysis, increased serum calcium levels are known to be associated with a poor prognosis. However, it is not known whether serum calcium levels at dialysis initiation have an impact on subsequent prognosis. Methods: The subjects were patients who were newly initiated dialysis at the 17 Aichi Cohort Study of Prognosis in Patients Newly Initiated into Dialysis (AICOPP) group centers. The study included 1524 patients who were at least 20 years old, had CKD, and provided written consent. We excluded one patient whose serum adjusted calcium was not assessed and six patients whose outcomes were unknown. Thus, we enrolled 1517 subjects into the study. The patients were divided into the following five groups: (1) G1 with a serum adjusted calcium level <7.0 mg/dL, (2) G2 with 7.0 to <8.0 mg/dL, (3) G3 with 8.0 to <9.0 mg/dL, (4) G4 with 9.0 to <10.0 mg/dL, and (5) G5 with ≥10.0 mg/dL. The study outcomes included: (1) comparisons of all-cause mortality rates in the five groups; (2) extraction of factors influencing all-cause mortality. Results: There were 268 deaths during the follow-up period (G1, 9 cases; G2, 30 cases; G3, 91 cases; G4, 110 cases; G5, 28 cases). Significant differences were observed between the five groups' cumulative survival rates (Logrank test p = 0.005) by using Kaplan-Meier method. There were significant differences in the incidence of either aortic or cardiac valve calcification among the five groups (aortic calcification: p = 0.006, cardiac valve calcification: p = 0.008). Moreover, lower Barthel Index, which evaluated activities of daily living, were associated with higher serum adjusted calcium levels (p < 0.001). Multivariate Cox proportional hazard analysis using the stepwise method indicated that increasing serum adjusted calcium was associated with all-cause mortality (every 1 mg/dL increase, HR = 1.267, 95% CI = 1.092 − 1.470, p = 0.002). In addition, high mortality was associated with advanced age, male gender, low systolic blood pressure, history of cardiovascular disease, and no prior use of calcium carbonate. Conclusions: Serum adjusted calcium levels at dialysis initiation were demonstrated to be associated with all-cause mortality after dialysis initiation.