Background Hepatitis B e antigen (HBeAg) and hepatitis B surface antigen (HBsAg) clearance are associated with an improved prognosis in chronic hepatitis B (CHB) patients. These end points are more often achieved with a one-year course of pegylated interferon (PEG-IFN) compared with one year of nucleoside/nucleotide analogue therapy. However, prolonged nucleoside/nucleotide analogue therapy may result in comparable serological response rates as with PEG-IFN. Methods We compared serological and virological response rates among HBeAg-positive CHB patients treated with long-term continuous entecavir (ETV; n=91) for a median of 92 (IQR 50–132) weeks or one year of PEG-IFN ( n=266) with comparable follow-up. Results Median follow-up was 92 weeks (IQR 78–198) for patients treated with PEG-IFN and 92 weeks (IQR 50–132) for patients treated with ETV. Finite PEG-IFN therapy resulted in significantly higher rates of HBeAg seroconversion (adjusted hazard ratio [HR] 3.16; P<0.001) and HBsAg clearance (HR 5.66; P=0.027) when compared to prolonged ETV treatment, whereas, ETV resulted in higher rates of HBV DNA undetectability (OR 31.14; P<0.001) also after adjustment for HBV genotype and other relevant baseline factors. Conclusions Our study shows that finite PEG-IFN is associated with a higher probability of serological, but not virological, response for HBeAg-positive CHB patients when compared to prolonged ETV, even after correction for baseline differences.