A subluxation or dislocation of the carpometacarpal joint of the thumb is a rare injury, which usually occurs from trauma. There is a relative dearth of literature about the results of hand surgery for the treatment of Ehlers-Danlos syndrome. To the best of our knowledge, there has been no report on capsular ligament reconstruction in the hand using an autogenous tendon graft for the treatment of Ehlers-Danlos syndrome. We describe a case of atraumatic dislocation of the carpometacarpal joint of the thumb that had gradually progressed in a patient with Ehlers-Danlos syndrome; and which was treated with capsular ligament reconstruction by use of a portion of the flexor carpi radialis tendon. Six months after surgery, a trapeziometacarpal arthrodesis was performed secondarily, because of subluxation and pain in the carpometacarpal joint of the thumb, with a pinching motion.