Despite higher risk for school failure, few school-based mentoring (SBM) studies have focused on low-income at-risk Latino children. We describe the development and evaluation of the Youth Empowerment Program (YEP), a sustainable, high-quality, SBM program among urban Latino students. Based on evidence from work in other communities, YEP was created as a partnership between the 4th and 5th grades at a Los Angeles Title I elementary school and university undergraduates. We tested the feasibility of applying a previously validated relationship quality assessment tool in this population. Since 2008, 61 mentor and mentee pairs have participated in YEP, with an average relationship length of 1.5 years. Through 2010, over 95 % of pairs had relationships lasting at least 1 year, while 47 % lasted 2 or more years. Seventy-percent of mentees and 85 % of mentors were female, and an increased trend for early relationship termination was observed among male mentees. Through 2011, relationships lasted under 1 year among 29 % of male mentees compared to 7 % of female mentees (p = 0.15). A previously validated relationship quality assessment tool was easily incorporated into YEP, with relationships exhibiting youth-centeredness, emotional engagement and low dissatisfaction. After 5 years, YEP has become a feasible and sustainable SBM program providing long-term relationships for low-income Latino children. These relationships may improve youth health through fewer risky behaviors and attitude improvements. Future work should focus on supporting male mentors and mentees.