Youth entrepreneurship is a promising field for employment and poverty alleviation for young people who the majority in the developing world. While effort has been made to promote entrepreneurship among the youth in Kenya and Uganda, most of it has been targeting urban youth who compromise a small proportion of the overall youth population in the two countries. Using a mixed methods approach of semi structured questionnaires and in-depth interviews; this paper provides a comparative assessment of Rural Youth Entrepreneurs (RYE) in Uganda and Kenya. More specifically it examines the entrepreneurial environment in which Ugandan and Kenyan RYE operate and identifies their unique challenges with a view of making policy recommendations to support them. Findings reveal that there are differences among RYE in both countries in the demographic aspects of gender, level of education, marital status and household headship. Nevertheless there are similarities when it comes to RYE perceptions of the business environment especially in terms of how they acquired their business, understanding the benefits of business registration, property rights and Justice Perceptions. Findings also revealed that both countries shared some challenges like limited access to funding and business skills training; while other challenges were country specific such as having unregistered businesses, high business closure rates and commercial injustice. Policy implications and recommendations are also provided.