Antiviral therapy is an essential treatment for chronic hepatitis B (CHB) infection. Although hypophosphatemia is an important adverse effect of antiviral agents, its clinical significance remains unclear. We investigated the incidence and clinical consequences of hypophosphatemia in a large cohort of CHB patients. Methods: This retrospective cohort study included CHB patients who started antiviral therapy between 2005 and 2015 and continued it for at least 1 year. Patients with decompensated liver cirrhosis, diabetes mellitus, hypertension, concomitant diuretic administration, and end-stage renal disease were excluded. The primary outcome was a change in renal function. Secondary outcomes included the incidence of infection and changes in serum potassium, uric acid, and total carbon dioxide (tCO2). Results: Among the 4,335 patients, hypophosphatemia developed in 75 (1.7%). During the median 2-year follow-up period, patients with hypophosphatemia showed a lower estimated glomerular filtration rate than those in the control group. The incidence of infection and changes in serum potassium, uric acid, and tCO2 were similar between groups. Conclusion: Hypophosphatemia was associated with a renal function decline in patients with CHB receiving antiviral therapy.