Abstract Background Maternal and infant HIV status influences the decision of BCG immunization of infants at birth. The objective of this study was to determine the HIV status of HIV-exposed infants (HEIs) by the first HIV DNA PCR test and the rate of BCG uptake among the HEIs who were confirmed HIV negative. Methods This was a retrospective descriptive cross-sectional study involving the review of results of 99 dried blood samples (DBS) for the first HIV DNA PCR test of HEIs whose mothers were diagnosed HIV positive on presentation of the infants at first immunization visit at a Primary Health Centre from January 2018 to January 2019. Results Of the 99 DBS examined, 86; 86.9% (95% CI 80.1–93.6) were HIV negative, 9; 9.1% (95% CI 3.3–14.8) were positive while the results of 4 (4.0%) infants were not in the register. Only 7; 7.1% (95% CI 1.9–12.2) of the 99 HEIs returned for BCG immunization at the centre. BCG immunization status of the HEIs after first PCR results was not significantly associated with sex of the infants or availability of phone number of the guardians (p = 0.70 and 0.12, respectively). Conclusion The majority of HEIs were HIV negative at first HIV DNA PCR test. Few of these HIV negative infants returned for BCG immunization. Hence, all HEIs should be given BCG immunization according to WHO GAVCS committee recommendation on BCG immunization for settings with poor HIV diagnostic and treatment facilities for mothers and infants.