Background: Decades of civil conflict compound the challenges of food insecurity in South Sudan and contribute to persistent, high levels of child malnutrition. As efforts to prevent child malnutrition continue, there is a critical need for strategies that effectively supplement the diets of pregnant women and young children in transitional, highly food insecure settings like South Sudan. Methods: This mixed-methods case study of four communities in South Sudan reports on the diets of children under 2 years of age and explores household-level factors including household size, intrahousehold food allocation practices, and responses to scarcity that may have significant impact on the effectiveness of strategies relying on household ration distribution to supplement the diets of pregnant women and children under 2 years of age. Results: Participants reported experiencing increased scarcity as a result of prolonged drought and household sizes enlarged by the high volume of returning refugees. Although communities were receiving monthly household rations through a non-emergency food assistance program, most households had exhausted rations less than 30 days after receipt. Results showed that more than one half of children 12-17 months and one third of children 18-23 months consumed diets consisting of fewer than 4 food groups in the last week. Intrahousehold food allocation patterns give children first priority at meal times even in times of scarcity, yet adult women, including pregnant women, have last priority. Discussion: These findings suggest that distribution of supplementary household rations will likely be insufficient to effectively supplement the diets of young children and pregnant women in particular. In light of the multiple contextual challenges experienced by households in transitional, food-insecure settings, these findings support recommendations to take a context-specific approach to food assistance programming, in which considerations of intrahousehold food allocation patterns and broader cultural and environmental factors inform program design. Incorporating assessments of intrahousehold food allocation patterns as part of needs assessments for food assistance and voucher or cash transfer programs may contribute to more effective, context specific programming.