Background and Objective: Morton’s syndrome (MS) is a common cause of neuropathic chronic forefoot pain, characterised by the development of a swelling of the common digital plantar nerve, whose aetiology is not fully known. There is currently no gold standard of treatment; nonoperative management commonly involves manual therapies, orthoses therapy and infiltrative techniques, while surgery is indicated after failure of conservative measures. The present preliminary study prospectively evaluates patients affected by MS treated by Fascial Manipulation technique (FM), a noninvasive manual therapy, focused on the release of the deep fascia, reducing its stiffness. Materials and Methods: Patients with clinical and sonographic diagnosis of MS with at least a 4-month history of neuropathic symptoms underwent a cycle of three weekly FM sessions. Clinical follow-up, including VAS and AOFAS scores, was performed 21 days (T1) and 3 months (T2) after treatment. Results: Nine patients, among 28 recruited initially, completed the manual therapy sessions and relative follow-up points. This noninvasive pain treatment led to significant improvement of VAS (p = 0.0034) and AOFAS scores (p = 0.0240) at the first follow-up (T1). At 3-month follow-up (T2), both scores decreased slightly, remaining however superior to the pre-treatment values. Only VAS was still significant (p = 0.0184). Conclusions: Despite the small size of the case series, this pilot study is unique in supporting Fascial Manipulation in the nonoperative treatment of MS. Further studies are needed with a large cohort of gender balanced patients to confirm the encouraging results obtained.