Background Occult hepatitis B virus (HBV) infections remain a safety concern worldwide. The prevalence in Kenya ranges from 2.6% to 4.4% among secondary school-going voluntary blood donors. This study estimated the prevalence of occult HBV infections among school-going voluntary blood donors through donations made to Kwale Satellite Blood Transfusion Center (KSBTC). Methods This was a retrospective cross-sectional study on data collected by the KSBTC between January 2020 and June 2021 among secondary school-going voluntary blood donors. Data were collected in MS Excel 2013 and analyzed in Epi Info 7. Descriptive statistics were calculated and we compared donors with positive Hepatitis B surface antigen (HBsAg) to those with negative HBsAg. Crude Prevalence Odds Ratios (cPOR) at 95% confidence intervals (CI) were calculated to identify factors associated with positive HBsAg. Results A total of 613 records were analyzed. The mean age of the donors was 19.1 years (± 1.8 years), there were 457 males (74.5%), 502 individuals were in the age group 18–25 years (82.3%), and the mean hemoglobin level was 14.1 g/dl (±1.6 g/dl). First-time blood donors made up 84.8% of all donors (513/605) and the mean inter-donation period was 20 months (±5.8 months) for repeat donors. The sero-positivity for HBsAg was 8.8% (54/613). Age category 16–17 years with positive HBsAg were 10.2% (11/108), femaleswere10.9% (17/156), and first-time donors were 9.4% (48/513). On bivariate analyses, first-time blood donors were 1.5 times more likely to test positive for HBsAg compared to repeat donors (cPOR = 1.5, 95% CI 0.61–3.57). Females were 1.4 times more likely to test positive for HBsAg compared to male donors (cPOR = 1.4, 95% CI 0.76–2.54). Conclusions The majority of the voluntary blood donors were males and the majority of occult HBV infections came in the first-time blood donor group. We recommend increasing targeted recruitment of repeat donors by encouraging healthy first-timer donors to be regular donors, and suggest this population should be vaccinated against HBV infections.