<i>Background</i>: Maternal and neonatal morbidity and mortality are major public health concerns in most developing countries and in under resourced settings. Increasing the proportion of babies that are delivered in health facilities is an important factor in reducing the health risks to both the mother and the baby. In Uganda’s skilled birth attendance is 58% of antenatal care mothers. <i>Objective</i>: The study assessed factors influencing the choice of place of delivery among women of reproductive age in Ngenge Sub County, Kween District- Sebei Sub region, Eastern Uganda. <i>Methodology</i>: The study design was cross-sectional in which data were collected using an interviewer administered structured questionnaire and analyzed using Epi info version 7.2. <i>Results</i>: A total of 350 mothers were interviewed of which 82% were married. Delivery under skilled attendance was 46%. Chances of delivering at the health facility decreased with increase in age (p=0.001), with increased parity (p=0.002), and increased with higher household income (p=0.011), and among mothers and their partners who had higher level of education (p=0.031, 0.024 respectively). The factors which influenced delivery in the health facility included: short waiting time at the health facility before receiving health care services, good attitude of the health care workers, and adequate birth preparedness during ANC. The factors which influenced delivery elsewhere included; the far distances to the nearest health facility, low education of mothers and their partners, increased maternal age, low household income, high parity, poor decision making and high perception of the mothers about the care provided by TBAs. <i>Conclusion</i>: The study concludes that skilled delivery was low at 46% way-below the national target of 95%. The factors statistically associated with choice of place of delivery included: waiting time at the health facility, attitude of the health care workers, birth preparedness during ANC, distance to the nearest health facility, level of education of mothers and their partners, maternal age, household income, parity of mothers, decision making, and perception of the mothers about the care provided by TBAs.