BACKGROUND: People with migraine often experience disability with serious consequences for their social life and work productivity. The pharmacological prophylactic management of migraine is effective in reducing migraine attacks. However, many people are reluctant to use daily prophylactic medication, leading to a demand for non-pharmacological treatment options. We present the design for and discuss the feasibility of a pragmatic, randomized controlled trial on the effectiveness of a multimodal manual therapy (MT) treatment compared to usual care by the general practitioner (GP) for the prophylactic treatment of migraine. METHODS: Eligible participants will be recruited in primary care using the International Classification of Headache Disorders III criteria for migraine of the International Headache Society. Participants will be randomized to either multimodal MT treatment or usual care provided by the GP. GPs will be asked to treat the usual care group according to the Dutch GP guideline for headache. The multimodal MT intervention will include manual pressure techniques, neck muscle-strength exercises and mobilization of the cervical and thoracic spine. The trial will consist of a 12-week treatment period and follow-up measurements at 12, 26 and 52 weeks. The primary outcome measure is the number of migraine days per 4 weeks, assessed with a headache diary. Secondary outcome measures are the number of migraine attacks, medication use, disability due to headache, headache intensity, number of participants reporting a 50% migraine reduction, measurement of cervical pressure pain thresholds, presence of allodynia, endurance of cervical flexor muscles, days of absence of work and global perceived effect. DISCUSSION: The results of the trial will show whether a multimodal MT intervention is an effective non-pharmacological treatment option for people with migraine. TRIAL REGISTRATION: Dutch Trial Register, NL7504. Registered on 7 February 2019.