© 2022 by the authors.Burkholderia cepacia complex (BCC) is a rare cause of sepsis in neonates, but infections are usually severe. It can be encountered unexpectedly when adequate health care is not provided. In this study, 49 neonatal cases with blood culture-proven BCC bacteremia within the first 72 h following admission to the neonatal intensive care unit between June 2017 and December 2018 were retrospectively analyzed in detail. All but one of the cases were born in Jarabulus, Al Bab, or Aleppo in Syria and were referred to Turkey due to urgent medical treatment needs. The rate of BCC bacteremia among the neonates transferred from across the border was 16.1% (48/297). The most common coexisting problems in the cases were multiple congenital malformations (12.2%), gastrointestinal system atresia (8.2%), and congenital heart diseases (4.1%). The median age at the time of their admission in Turkey was three days, and the median length of stay in another center before the referral was 11.5 h. The case fatality rate was 14.3%. In this study, a high rate of BCC infection and associated mortality was seen in neonates referred from cross-border regions. For centers accepting cases from conflict-affected regions, it is crucial to be careful regarding early detection of bacteremia, planning appropriate treatments, and preventing cross-contamination risks within the unit.