A total of 31,485 Syrian refugee households have been reached by the Medair nutrition programme covering 35% of the estimated number of refugees in Jordan urban areas. In April of 2014, a household survey was conducted to estimate exclusive breastfeeding (EBF) rates among those households reached by Medair with IYCF messages. 990 out of 31,485 households were selected by systematic random sampling for a telephone survey. Among those sampled, 12.9% (128 households) had children less than 6 months of age; 24.2 ± 7.7% of these reported practicing exclusive breastfeeding within the previous 24 h. This value is much lower than levels of EBF reported in Syria prior to the crisis (42.6%) despite effective IYCF promotion activity reflected by the fact that 71.3% (± 6.4%) of lactating mothers surveyed were able to state more than two benefits of EBF covered. Considering EBF is one of the most effective way to save the lives of young children, this deterioration in EBF among refugees placing young children at an increased risk of death should serve as a warning to the humanitarian community that measures to improve EBF is needed immediately. Additionally the survey implies other interventions are needed to address the other potential obstacles to EBF practices such as cultural and social barriers. Group sessions to monitor the barriers and promoters of IYCF as well as developing a self-supporting system among caregivers influencing the social and cultural aspects of EBF may be helpful to facilitate dissemination of lessons learned among the refugee communities.