Our study looks at the effects of burnout and stress levels of nurses, behaviour regarding medical waste, and other effective risk factors on the first time and recurrent diagnosis of nosocomial infection (NI) in neonatal intensive care units in Hargeisa, Somaliland. This multicentric follow-up study was conducted and repeated measurements were taken from 72 neonates and 45 nurses working in three hospitals for a period of five months. Nurses with high burnout levels had 3.7 times higher risk of neonates under their care being diagnosed with an NI (odds ratio: 3.743; 95% CI: 1.498-9.356). By controlling other variables, the stress level of nurses increased the incidence rate of neonates being diagnosed more than once with NI by 3.2 times. Statistically, the direction of causal association was from the high burnout among nurses to the diagnosis of NI, and high stress was associated with the recurrent diagnosis of infections in neonates.