Migraine is one of the most common neurological disorders in clinical practice and is a substantial cause of disability worldwide. Current approaches to therapy are primarily based on medication but are often limited by inadequate effectiveness and common side effects. Newer, more effective medications are expensive. Mindfulness-based stress reduction (MBSR), an 8-week classroom-based meditation intervention, is inexpensive, has no known side effects, and has demonstrated clinically meaningful effectiveness for several chronic-pain syndromes. In addition, MBSR has shown promising results for migraine therapy in a few small case studies and pilot studies. We present here the protocol for a two-arm randomized controlled pilot trial of MBSR for moderate-to-severe episodic migraine, which, if successful, will form the basis for a fully powered clinical trial. This study, set in Northern California, is a two-arm parallel-comparison single-blinded randomized controlled pilot trial with the goal of recruiting approximately 60 participants with moderate-to-severe episodic migraine. The feasibility outcomes include ability and time required to recruit, adherence to the MBSR treatment, and ability to measure outcomes using 31-day headache diaries and patient-reported questionnaire data. The active treatment arm consists of an 8-week community-based MBSR class plus usual care, and the wait-list control group is usual care. Recruitment is underway and expected to be complete by the end of 2018. To our knowledge, this is the first pragmatic trial in the U.S. of MBSR for migraine using community-based classes, and if it proves viable, we plan to conduct a fully powered trial to determine the effectiveness of the intervention for reducing headache days for moderate-to-severe episodic migraineurs. Clinicaltrials.gov, NCT02824250 . Registered on 6 July 2016.