The aim of this study was to investigate the immediate and long-term effects of a one-year multimodal program, with the addition of upper cervical manipulative therapy, on fibromyalgia management outcomes in addition to three-dimensional (3D) postural measures. This randomized clinical trial with one-year follow-up was completed at the research laboratory of our university. A total of 120 (52 female) patients with fibromyalgia syndrome (FMS) and definite C1-2 joint dysfunction were randomly assigned to the control or an experimental group. Both groups received a multimodal program; additionally, the experimental group received upper cervical manipulative therapy. Primary outcomes were the Fibromyalgia Impact Questionnaire (FIQ), whereas secondary outcomes included Pain Catastrophizing Scale (PCS), algometric score, Pittsburgh Sleep Quality Index (PSQI), Beck Anxiety Inventory (BAI), Beck Depression Inventory (BDI), and 3D postural measures. Measures were assessed at three time intervals: baseline, 12 weeks, and 1 year after the 12-week follow-up. The general linear model with repeated measures indicated a significant group × time effect in favor of the experimental group on the measures of 3D postural parameters (P < .0005), FIQ (P < .0005), PCS (P < .0005), algometric score (F = P < .0005), PSQI (P < .0005), BAI (P < .0005), and BDI (P < .0005). The addition of the upper cervical manipulative therapy to a multimodal program is beneficial in treating patients with FMS.