Obtaining a better understanding of the mechanisms associated with hepatitis B surface antigen (HBsAg) and hepatitis B e antigen (HBeAg) loss in patients with hepatitis B virus (HBV) is important for treating patients with chronic hepatitis B. We herein describe the case of a patient with HBV and human immunodeficiency virus whose chronic hepatitis was stabilized due to HBe and HBs seroconversion with the emergence of lamivudine-associated and core mutations after CD4 elevation. A full-length HBV DNA analysis indicated that HBsAg had been lost after the development of the rtS143T mutation, which corresponded to the emergence of the sF134L and core mutations. The details of this case shed some light on the mechanisms associated with HBsAg and HBeAg clearance.