Neuroma surgery is performed when the non-surgical treatment of this condition fails to fully relieve the pain on a long-term basis. The procedure itself is fairly simple, and involves removal of a section of the nerve causing the pain. An incision is typically made on top of the foot, to avoid a potentially painful scar on the bottom of the foot. The ligament binding the bones on either side of the nerve is released, which releases pressure on the nerve itself. In a small percentage of cases, this may be enough to provide relief. For most other cases, the surgery continues and the nerve with the inflamed section is identified. The nerve section is then removed, starting as far back as possible in the mid section of the foot and going all the way up to where the nerve branches into the two toes it provides sensation for. Each cut end is allowed to nestle back into muscle tissue to avoid the development of a stump neuroma, which is a new neuroma formed at the cut end of a nerve allowed to sit in open space. The ligament is then left released to reduce pressure to the area, and the skin is then repaired.

Recovery from neuroma surgery is usually uneventful. A dressing is used to allow the incision to heal, and a supportive surgical shoe supports the foot during healing. Most patients can return to a regular shoe and regular activities within three to four weeks. If one is too active the week following surgery, the space previously occupied by the nerve can fill with fluid, leading to pain and inflammation. Icing, rest, and elevation of the foot easily prevents this from occurring. The previous pain felt by the neuroma is replaced by permanent numbness under the involved toes. This patch of numbness is narrow, only generally noticed upon stroking the skin, but is unfortunately unavoidable. However, those who suffer from this condition gladly accept this minor focused sensory loss as opposed to the pain.