Purpose: An inverse association was shown between serum magnesium levels and anemia in the general population. However, limited information is available about the association between serum magnesium level and anemia in the patient population with chronic kidney disease. We aimed to investigate the relationship between hypomagnesemia and anemia in pre-dialysis patients with chronic kidney disease stage 3–5. Methods: This cross-sectional retrospective study included 213 chronic kidney disease patients with an estimated glomerular filtration rate of 60 mL/min and below. Laboratory and demographic data of outpatients were collected in January 2018—January 2019. Patients with a magnesium level below 1.9 mg/dL were accepted as the hypomagnesemia group. Results: Serum magnesium level of 62 (29.1%) of these patients were below 1.9 mg/dL. Compared with normomagnesemic patients, hypomagnesemic patients had lower mean hemoglobin values (11.3 g/dL vs. 12.7 g/dL, P ' 0.001), proton-pump inhibitor usage rates were significantly higher (33.9% vs. 17.2%, P = 0.008) and the median urine protein/creatinine ratio was found to be significantly higher (1017.5 mg/gCr vs. 536 mg/gCr, P = 0.045). In the multivariate analysis, the use of hemoglobin (OR 0.634; 95% CI 0.505–0.795; P ' 0.001) and proton-pump inhibitor (OR 2.670; 95% CI 1.113–6.318; P = 0.025) were independent predictors of hypomagnesemia. Conclusions: Hypomagnesemia is a common electrolyte disorder in pre-dialysis CKD patients. In this patient group, anemia is independently associated with hypomagnesemia.