A country of 64 ethnic groups, South Sudan is deeply divided along ethnic lines; this has permeated throughout the social, economic, and political fabric of the country. This minor field research was conducted to investigate the challenges NGOs face managing ethnic diversity. The study investigated the influence of ethnic diversity on staff recruitment and selection and how NGOs manage ethnically diverse staff, the challenges they face and how they manage these challenges. The study also interviewed some unemployed public on their views and opinions on whether ethnic diversity in the country has any influence in their possible recruitment in the NGO sector. The results of the study showed that ethnicity does have a great influence on recruitment and selection even in the NGO sector. This finding is consistent with views of social identity theory which suggest that individuals and groups do define and categorise themselves based on perceived similarities which are used for distinguishing or differentiating themselves from other groups. The study further revealed that the two selected NGOs in the study do face significant challenges managing an ethnically diverse workforce.