BACKGROUND: Major depression is a common psychiatric disorder, frequently taking a chronic course. Despite provision of evidence-based treatments, including antidepressant medication and psychological treatments like cognitive behavioral therapy or interpersonal therapy, a substantial amount of patients do not recover. Mindfulness-Based Cognitive Therapy (MBCT) has been found to be effective in reducing relapse in recurrent depression, as well as lowering symptom levels in acute depression. The effectiveness of MBCT for chronic, treatment-resistant depression has only be studied in a few pilot trials. A large randomized controlled trial is necessary to examine the effectiveness of MBCT in reducing depressive symptoms in chronic, treatment-resistant depression. METHODS/DESIGN: A randomized-controlled trial is conducted to compare MBCT with treatment-as-usual (TAU). Patients with chronic, treatment-resistant depression who have received antidepressant medication and cognitive behavioral therapy or interpersonal therapy are included. Assessments take place at baseline and post intervention/TAU-period. The primary outcome are depressive symptoms. Secondary outcomes are: remission rates, quality of life, rumination, mindfulness skills and self-compassion. Patients in the TAU condition are offered to participate in the MBCT after the post TAU-period assessment. From all completers of the MBCT (MBCT condition and patients participating after the TAU-period), follow-up assessments are taken at three and six months after the completion of the MBCT. DISCUSSION: This trial will result in valuable information about the effectiveness of MBCT in chronic, treatment-resistant depressed patients who previously received antidepressant medication and psychological treatment. TRIAL REGISTRATION: trialregister.nl NTR4843, registered 14th October 2014.