There is a growing demand for health sciences faculty with formal training in education. Addressing this need, the University of Michigan Medical School created a Master in Health Professions Education (UM-MHPE). The UM-MHPE is a competency-based education (CBE) program targeting professionals. The program is individualized and adaptive to the learner's situation using personal mentoring. Critical to CBE is an assessment process that accurately and reliably determines a learner's competence in educational domains. The program's assessment method has two principal components: an independent assessment committee and a learner repository. Learners submit evidence of competence that is evaluated by three independent assessors. The assessments are presented to an Assessment Committee who determines whether the submission provides evidence of competence. The learner receives feedback on the submission and, if needed, the actions needed to reach competency. During the program's first year, six learners presented 10 submissions for review. Assessing learners in a competency-based program has created challenges; setting standards that are not readily quantifiable is difficult. However, we argue it is a more genuine form of assessment and that this process could be adapted for use within most competency-based formats. While our approach is demanding, we document practical learning outcomes that assess competence.