Background: Permanent congenital hearing loss affects up to 6/1000 births in developing countries. Currently, in Uganda there is no newborn screening for hearing loss (NSHL) program and no published work on this topic. Within the existing healthcare system there are two opportunities to deliver screening, at birth or 6 weeks of age when infants receive their immunizations. Aim: This study explored the outcomes of otoacoustic emission (OAE) testing in infants at birth and 6 weeks of age, to identify the optimal age for screening. Subjects and Methods: This cross-sectional pilot study recruited 60 consecutive infants from two health centres in Kampala, Uganda. Thirty infants were newborns recruited from the postnatal ward and 30 were aged 4–8 weeks from the immunization clinic, we performed OAE testing on all infants. Results: The results showed 56.7% (17/30) of newborn infants passed OAE testing compared with 90.0% (27/30) of the immunization infants, P < 0.01. Furthermore, of the 11 newborn infants aged ≥24 h of age 90.9% (10/11) passed, compared with the 19 infants <24 h of age where 37% (7/19) passed, P < 0.01. Conclusions: This study demonstrates a higher pass rate for OAE testing for infants ≥24 h of age compared to those <24 h of age. The overall lower pass rate of the newborn infants could be due to external ear debris and middle ear fluid compromising the OAE testing. These findings would support a NSHL programme in Uganda that offers screening to infants ≥24 h of age, to maximize the cost-effectiveness of the program.