Increasingly, community-based participatory research (CBPR), with its emphasis on engaging communities as full and equal partners in all phases of the research process is being promoted to address the health needs of peoples living in the North American Arctic. However, the CBPR approach is not without its challenges in Arctic countries such as Greenland, where research capacity, different languages, distance, time and cost become barriers to remaining true to the purest form of CBPR. In this paper, we describe the practical application of CBPR principles and methodologies to a sexual health project investigating sexually transmitted infections in Greenland. We present the initial challenges encountered in the early stages of the pilot CBPR sexual health study, and solutions to these challenges. We also provide recommendations for expanding the capacity in Greenland to conduct CBPR projects.