Abstract Background The hepatitis A virus (HAV) is the most frequent global causes of vaccine-preventable viral hepatitis. Since Somalia is regarded as highly endemic for hepatitis A, the hepatitis A vaccine was not included in the World Health Organization’s expanded immunization program. The purpose of this study was to determine the prevalence of hepatitis A infection in the Somalia capital, Mogadishu. Methods The serological results of 1153 individuals presenting to the Mogadishu Training and Research Hospital between January 2019 and January 2021 were examined retrospectively to evaluate the presence of anti-HAV IgG and IgM. The seroprevalence of anti-HAV IgG and IgM was analyzed on the basis of age and sex. The seroprevalence of anti-HAV IgG was also compared among the 11-year age group. Findings The seroprevalence of anti-HAV IgG and IgM did not vary significantly between the sexes. Overall, the seroprevalence of anti-HAV IgG was 67.6%. The percentage of seropositivity for anti-HAV IgG was highest in adults aged ≥41 years (88.9%) and lowest in children aged 1–2 years (29.4%). Estimated age at midpoint of population immunity was 5 years which is compatible high endemicity. In addition, a significant rate of hepatitis A infection was also observed in the adolescent age group. Conclusions This study confirms the high HAV endemicity in Mogadishu. These data will be useful towards planning preventive and control measures by improving the sanitation programs in Mogadishu. Furthermore, prospective studies are needed to confirm these findings and evaluate urban–rural heterogeneity.