Purpose To investigate the topological organization of functional brain networks in clinically isolated syndrome (CIS) and multiple sclerosis (MS) and examine the clinical relevance. Materials and Methods The institutional review board of Xuanwu Hospital, Capital Medical University, Beijing, People's Republic of China, approved the study, and written informed consent was obtained from each participant. Functional brain networks were constructed for 34 patients with MS, 34 patients with CIS, and 36 matched healthy control subjects by using resting-state functional magnetic resonance (MR) imaging data. Graph-based network measures were then calculated, followed by performance of between-group comparison and brain-behavior correlation analysis. Results Decreased whole-brain network efficiency was observed for patients with MS when compared with healthy control subjects, with intermediate values for the patients with CIS (P < .05, corrected). Regionally, both patient groups showed decreased nodal efficiency in the left rolandic operculum and insula and the superior temporal gyrus of the bilateral temporal pole (P < .05, corrected). Moreover, impaired functional connectivity involving the occipital, temporal, and frontal cortices and the insula was identified in MS (P = .007), and a similar but smaller component was observed in CIS (P = .032). The disrupted functional connectivity correlated with disease duration of the patients (r = 0.312, P = .011) and served to distinguish the patients from healthy control subjects with high performance (area under the curve for MS, 0.825 [P < .001]; area under the curve for CIS, 0.789 [P < .001]). These findings were reproducible across several different analytical strategies and were largely independent of white matter lesions and gray matter atrophy. Conclusion The results of this study demonstrate that disrupted network organization already emerges in CIS, with a lesser degree relative to MS. © RSNA, 2016 Online supplemental material is available for this article.