Hepatitis B virus (HBV) remains a major public health challenge in low- and middle-income countries. Burkina Faso, with a national prevalence of 9.3%, is highly endemic. Despite the introduction of DTP-HepB-Hib vaccine in 2006 and WHO recommendations for universal vaccination, coverage remains suboptimal in sub-Saharan Africa. Some vaccinated children and adolescents exhibit sub-protective antibody levels. This study evaluated HBV seroprevalence in children born after 2006, vaccination coverage, and the proportion of vaccinated children with protective anti-HBs antibodies in Burkina Faso. A cross-sectional descriptive study was carried out from 2021 to 2025 in schools and health centers in Ouagadougou, where blood samples (N = 1384) from children and adolescents born after January 2006 were collected. Rapid diagnostic tests (RDTs) were used to determine HBV seroprevalence and enzyme linked-immunosorbent Assay (ELISA) was used for titration of anti-HBs antibodies in children and adolescents. The Student’s test was used for the comparison of quantitative variables and the Chi² test for the comparison of proportions with 5% as the statistical significance threshold. The study population consisted of 41.47% males. The average age was 8.96 ± 4.5 years. The prevalence of hepatitis B in our study population was 4.34%. The prevalence of hepatitis B was significantly impacted by age (p = 0.008). The vaccination coverage rate was 90.47%. The prevalence of hepatitis B varied significantly with anti-HBS antibody titration (p < 0.001). The difference of anti-HBs antibody titration was significant between age groups (p < 0.001). Despite satisfactory vaccination coverage, HBV prevalence remains high among children and adolescents.