Military Veterans with Gulf War Illness (GWI), a “medically unexplained” persistent physical syndrome (PPS), have difficult experiences of care, in part, due to non-concordant relationships with their healthcare providers. A critical factor in improving care for this population may be the working alliance, which is the extent to which patients and providers agree on the goals and tasks of treatment and have a shared bond. The present study examined if, for Veterans with GWI, perceptions of the working alliance over time predicted better experiences of care (i.e., patient satisfaction and treatment adherence) and improved health outcomes (i.e., reduced disability, depression symptoms, and physical symptoms). Positive Veteran perceptions of the working alliance at 4 weeks were related to better patient satisfaction and treatment adherence at 12 weeks. Veteran perceptions of the working alliance were not consistently related to reductions in disability, depression symptoms, or physical symptoms. The results of this study suggest that the working alliance is important for improving patient experiences of care but may not be sufficient to consistently impact health outcomes.