Muscle fatigue is considered to be one cause of shoulder pain, and subjects with generalized joint hypermobility (GJH) are affected more by shoulder pain. The purpose of this study was to examine the effects of muscle fatigue on acromiohumeral distance (AHD) and scapular dyskinesis in women with GJH. Thirty-six asymptomatic participants were assigned to either a GJH (n = 20) or control group (n = 16) using the Beighton scale. Before and after elevation fatigue trials, AHD was measured with ultrasonography at rest and when the arm was in 90° active elevation. A scapular dyskinesis test was used to visually observe alterations in scapular movement. Our results showed that in both groups, the fatigue reduced AHD in the 90° elevation position and increased the presence of scapular dyskinesis; however, no differences were found between the two groups. Although GJH has been identified as a factor for developing musculoskeletal disorders, generalized joint hypermobility did not result in changes to scapular dyskinesis or AHD, even after an elevation fatigue task. More studies are needed to evaluate the effects of muscle fatigue in subjects with GJH and a history of shoulder instability.