Migraine is a highly prevalent episodic and chronic neurological disorder that impacts otherwise healthy men and women in their most productive years. An anecdotal survey in our clinical practices suggested that milnacipran, a drug indicated for the treatment of fibromyalgia, reduced the incidence of headache in patients with migraine. In this 3-month, open-label, pilot study, 38 patients diagnosed with episodic migraine and 7 patients with chronic migraine maintained headache diaries to assess the effectiveness and tolerability of milnacipran in headache prevention. After a 1-month period to obtain baseline data, milnacipran treatment was initiated and doses were titrated up to 100 mg/day over 1 month. Maintenance therapy continued for an additional 3 months. The primary efficacy end point was change from baseline in the number of all headache days during the last 28 days of maintenance therapy analyzed, using last observation carried forward (LOCF). Change from baseline in migraine days during the last month of the maintenance period using LOCF was a secondary end point. Milnacipran 100 mg daily was associated with a significant reduction in headache (-4.2 days; P < 0.001) and migraine frequency (-2.2 days; P < 0.003). The adverse event profile was consistent with prior reports of milnacipran for the treatment of other conditions. However, compared with the recommended protocol, a more gradual increase in milnacipran dose was required to improve tolerability for some patients. The robust efficacy signal found in this study strongly suggests that a double-blind, placebo-controlled trial of milnacipran in migraine and chronic headache is warranted.