Milestones, which provide a narrative description of the knowledge, skills and attitudes that a learner must progressively demonstrate throughout their training in order to enter unsupervised practice, represent the most recent method by which learner competency is measured in US graduate medical education. Milestones were recently developed for the fellowship in Complex Family Planning using a Delphi approach. Milestone assessment and demonstration of competence necessitates a system involving the assessor, the learner and validated assessment tools which reflect the milestone content. Learners develop a milestone-based individualized learning plan, which is re-visited and adjusted every 6 months incorporating input from multiple assessors, collected and aggregated using healthcare education management software. We provide the newly developed fellowship milestones as an example of a process educators can use to create milestones for their unique learning programs. A similar system, incorporating mastery-based learning principles, can be implemented for procedural skills training outside of the traditional graduate medical education environment.