Hepatitis B (HB) is an important public health problem affecting millions of people globally and is endemic in Nigeria. The objective of this study was to determine the effectiveness of the HB vaccine five to seven years post-introduction within a rural community in Nigeria. The study design was cross-sectional. Eligible children were either vaccinated subjects who had received at least two doses of HB vaccine or unvaccinated subjects (controls) who had not received HB vaccine. Following informed consent obtained from mothers/care givers, data was obtained using an interviewer-administered questionnaire. Venous blood was obtained to measure HB markers including hepatitis B surface antigen (HBsAg), and antibodies to the core (anti-HBc) and antibody to the hepatitis B surface (anti-HBs) antigens. Eight hundred and twenty-two subjects were eligible for analysis consisting of 449 vaccinated and 373 controls. The prevalence of anti-HBc was 43.2% in unvaccinated children compared to 10.5% in vaccinated children (p < 0.001). The rate of HBsAg was 11.8% in the unvaccinated group and 2% in the vaccinated group (p < 0.001). The vaccine effectiveness against anti-HBc was 84.6% (95% confidence interval 77.8, 89.3%) and the effectiveness against infection was 84.7% (95% confidence interval 68.2, 92.6%). Sixty-one percent of vaccinated subjects had protective antibodies ≥10 EIU/ml compared to 18% of controls (p < 0.001) and the geometric mean titers (GMT) were 19.96 and 7.28 EIU/ml respectively (p < 0.001). Vaccinated subjects were protected at least for five to seven years following HB vaccination.