The oculomotor system plays an important role in the development of migraines. This is an observational study that aims to investigate the rehabilitative efficacy of muscle energy therapy (MET) in reducing migraine symptoms. MET was based on post-isometric relaxation and reciprocal inhibition, targeting the extraocular muscles. Patients diagnosed with chronic migraines and positive results in the Smooth Pursuit Eye Movement Test were enrolled in the study. The effects of treatment were assessed using the following questionnaires: Migraine Disability Assessment (MIDAS), Neck Disability Index (NDI), Pittsburg Sleep Quality Index (PSQI), Dizziness Handicap Inventory (DHI), and the neck range of motion (ROM). Additionally, rheological parameters of neck muscles were assessed. We reported beneficial effects of MET on the amelioration of the frequency of headaches, neck pain and dizziness-related disabilities and disordered sleep. However, benefits concerning the neck motion and rheological properties of oculomotor structures were unconvincing. In conclusion, the study showed advantageous effects of manual oculomotor therapy consisting of reductions in migraine-related painful symptomatology. The results diminish the role of ocular muscle mechanical properties in the genesis of migraine, shifting attention to the modulatory role of the neuromuscular ocular component, likely involving trigeminal innervation, which can be subject to migraine manual therapy.