BACKGROUND: The highest neonatal mortality is in Sub-Saharan Africa, where neonatal sepsis accounts for approximately 50%. At Pemba Island, Tanzania, we examined the use of prophylactic antibiotics in neonates and related it to WHO guidelines and compared clinical signs of infection with the use of antibiotic treatment; furthermore, we aimed to investigate all use of antibiotic treatment in the neonatal period. METHOD: This prospective observational cohort study was performed from 1 January 2022 to 15 April 2022 at a district hospital on Pemba Island, Tanzania. Women admitted in early established or active labour, and their neonates, were eligible for inclusion. We used questionnaires for mother and health worker and examined the neonates 2 h after birth. Follow-up was made at discharge or at 18 h of life, and days 7 and 28. RESULTS: We included 209 women and their 214 neonates. The neonatal mortality was 5 of 214 (23 per 1000 live births). According to WHO guidelines 29 (13.6%) had ≥ 1 risk factor for infection. Of these, three (10.3%) received prophylactic antibiotic treatment; only one (3.4%) received the correct antibiotic drug recommended in guidelines. Thirty-nine (18.2%) neonates had ≥ 1 clinical indicator of infection and 19 (48.7%) of these received antibiotic treatment. A total of 30 (14.0%) neonates received antibiotics during the study period. Twenty-three (76.7%) were treated with peroral antibiotics. CONCLUSION: Adherence to WHO guidelines for prophylactic antibiotic treatment to prevent neonatal infection was low. Further, only half of neonates with clinical signs of infection received antibiotics.