BackgroundInfants born to HIV-infected mothers are at a high risk of acquiring the infection. The World Health Organization recommends early diagnosis of HIV-exposed infants (HEIs) through deoxyribonucleic acid polymerase chain reaction (DNA PCR) and rapid HIV testing. Early detection of paediatric HIV is critical for access to antiretroviral therapy (ART) and child survival. However, there is limited evidence of the factors associated with receiving early infant diagnosis (EID) tests of the HIV testing protocol among HEIs in fishing communities in Uganda. This study established the factors associated with receiving EID tests of the HIV testing protocol among HEIs in a hard-to-reach fishing community in Uganda.MethodsA cross-sectional study was conducted among HEIs in selected healthcare facilities in Buvuma islands, Buvuma district. We obtained secondary data from mother-infant pair files enrolled in the EID program using a data extraction tool. Data were analysed using STATA Version 14. A modified Poisson regression analysis was used to determine the factors associated with not receiving the 1stDNA PCR test among HEIs enrolled in care.ResultsNone of the HEIs had received all the EID tests prescribed by the HIV testing protocol within the recommended time frame for the period of January 2014-December 2016. The proportion of infants that had received the 1stand 2ndDNA PCR, and rapid HIV tests was 39.5%, 6.1%, and 81.0% respectively. Being under the care of a single mother (PR = 1.11, 95% CI: 1.01–1.23, p = 0.023) and cessation of breastfeeding (PR = 0.90, 95% CI: 0.83–0.98, p = 0.025) were significantly associated with not receiving the 1stDNA PCR.ConclusionOur study revealed that none of the HEIs had received all the EID tests of the HIV diagnosis testing protocol. Receiving the 1st DNA PCR was positively associated with being an infant born to a single mother, and exclusive breastfeeding. Our findings highlight the need for the creation of an enabling environment for mothers and caregivers in order to increase the uptake of early diagnosis services for HEIs. Awareness-raising on the importance of EID should be scaled up in fishing communities. Demographic characteristics such as marital and breastfeeding status should be used as an entry point to increase the proportion of HEIs who receive EID tests.