Attaining the target of <0.1% HBsAg positives in children aged <5 years in vaccinated populations by 2030 is a WHO indicator of hepatitis B elimination. We aimed to calculate the prevalence of HBsAg- and anti-HBc-positive children and adolescents in the low-prevalence country of Germany. In total, 3567 children and adolescents aged 3–17 years participated in a national population based cross-sectional study. Data were collected between 2014 and 2017 using questionnaires and health examinations, including blood samples. Applying a weighted analysis to account for survey design and participant characteristics, we calculated the HBsAg and anti-HBc prevalence and described them by anti-HBs positivity. In total, 3007 participants had all three sero-markers measured. None were found HBsAg and anti-HBc positive. Seven (0.3%, 95% CI: 0.1–0.8) were anti-HBc positive and HBsAg negative; six were also anti-HBs positive. All anti-HBc-positive participants were aged ≥7 years and three had no migration background. Four anti-HBc-positive participants had known vaccination status; three had been vaccinated according to national recommendations. This very low hepatitis B virus sero-prevalence among children and adolescents indicates that Germany is reaching some hepatitis B virus elimination targets. We recommend maintaining preventive measures, in particular a high vaccination coverage, in order to reach hepatitis B elimination.