Frailty is common among hemodialysis patients and is associated with mortality and fractures. Hypomagnesemia is also known to be a risk factor for mortality and fractures and has been shown to be significantly associated with muscle performance indexes. However, little is known about the association between hypomagnesemia and frailty. We enrolled 339 outpatients who underwent hemodialysis and assessed frailty using the Clinical Frailty Scale (CFS), a 7-point subjective assessment tool based upon clinical judgment. We examined the association between serum magnesium levels and frailty evaluated using the CFS. The median CFS score was 3 points, and 49 (14.5%) patients had frailty (CFS score ≥ 5). In multiple regression analysis, serum magnesium levels were independently associated with increased CFS scores (β = − 0.126, P = 0.005) adjusted for age, body mass index, diabetes, cardiovascular diseases, prevalent fractures, serum albumin and C-reactive protein. The adjusted odds ratio for frailty was 2.85 [95% confidence interval (CI) 1.23–6.97, P = 0.014] in the lower serum magnesium group categorized based on the median value. Furthermore, with regard to model discrimination, adding serum magnesium levels to the established risk factors significantly improved net reclassification (0.520, P < 0.001) and integrated discrimination (0.023, P = 0.031). Lower serum magnesium levels may be associated with the severity and definition of frailty independent of well-known risk factors.