Objective: Autologous bone marrow stem cell (ABMSC) transplantation has been considered a promising option for hepatitis B virus-related cirrhosis (HBV-C). Although an analysis of the published literature has been performed, the exact effects and safety have yet to be systematically investigated. Methods: We conducted a wide-ranging online search of electronic databases (Web of Science, PubMed, Cochrane Library, Embase, CNKI, VIP, and Wanfang database) to reach systematic conclusions. Outcome measurements, including therapeutic efficacy, clinical symptoms, and adverse events, were extracted and analyzed statistically. Results: Ultimately, a total of 10 articles including 662 HBV-C patients were included in this analysis, which indicated that ABMSC therapy could significantly improve liver function in patients with HBV-C in terms of the MELD and Child-Pugh scores, total bilirubin, serum albumin, alanine aminotransferase, aspartate aminotransferase, and coagulation function. Compared with patients receiving routine therapy (RT), those treated with ABMSC and RT combined therapy showed improved clinical symptoms, as represented by increased appetite and reduced fatigue and ascitic fluid and abdominal distension. Moreover, the fibrosis indexes indicated a reduction in liver fibrosis in patients treated with combined therapy according to the improved levels of hyaluronic acid (MD = − 70.47, CI = − 103.72-37.21, P < 0.0001), laminin (MD = − 25.11, CI = − 37.73-12.49, P < 0.0001), type III procollagen (MD = − 22.42, CI = − 34.49-10.34, P = 0.0003), and type IV collagen (MD = − 22.50, CI = − 39.92-5.08, P = 0.01). No obvious adverse events occurred during ABMSC treatment. Conclusion: ABMSC transplantation via the hepatic artery was safe and effective in treating HBV-C without causing severe adverse events.