Background: Although the majority of American Indians/Alaska Natives reside in urban areas, there are very few randomized controlled trials analyzing culturally centered substance use prevention interventions for this population. Methods: We describe methods employed to recruit and retain urban American Indian/Alaska Native adolescents into a randomized controlled trial, which was focused on testing the potential benefits of a substance use prevention intervention for this population. We also report challenges encountered in recruitment and retention of participants and strategies employed addressing these challenges. Data collection occurred from August 2014 to October 2017. Results: We partnered with two community-based organizations in different cities in California. We utilized American Indian/Alaska Native recruiters from communities, placed flyers in community-based organizations, and asked organizations to post flyers on their web and social media sites. We also offered gift cards for participants. Our initial recruitment and retention model was moderately successful; however, we encountered five main challenges: (1) transportation, (2) increasing trust and interest, (3) adding research sites, (4) getting the word out about the project, and (5) getting youth to complete follow-up surveys. Strategies employed to overcome transportation challenges included shortening the number of sessions, offering sessions on both weekends and weekdays, and increasing bus tokens and transportation options. We hired more staff from American Indian/Alaska Native communities, added more research sites from our previously established relationships, and were more proactive in getting the word out on the project in American Indian/Alaska Native communities. We also utilized more field tracking and emailed and mailed survey invitations to reach more participants for their follow-up surveys. Because of our efforts, we were nearly able to reach our initial recruitment and retention goals. Conclusion: Although our research team had previously established relationships with various urban American Indian/Alaska Native communities, we encountered various recruitment and retention challenges in our study. However, by identifying challenges and employing culturally appropriate strategies, we were able to collect valuable data on the potential effectiveness of a substance use prevention intervention for urban American Indian/Alaska Native adolescents. Findings from this study assist toward the development of potentially successful strategies to successfully recruit and retain urban American Indian/Alaska Native adolescents in randomized controlled trials.