<h3>Objective:</h3> To investigate changes in time-varying functional connectivity (TVFC) over 2.5 years of follow-up in multiple sclerosis (MS) patients and their association with disability progression. <h3>Background:</h3> In MS patients, TVFC analysis showed abnormalities of the main functional networks, correlated with more severe clinical and cognitive disability. Preliminary evidence showed that MS-related cognitive decline was associated with progressive TVFC destabilization. However, the clinical relevance of longitudinal TVFC changes has not been investigated yet. <h3>Design/Methods:</h3> 3T-MRI scans and clinical evaluations were obtained at baseline and at median follow-up of 2.5 years from 129 right-handed MS patients (103 relapsing-remitting [RR] and 26 progressive [P]) and 28 matched healthy controls (HC). At 2.5-year follow-up, patients were classified as clinically stable/worsened according to their disability change. TVFC was quantified at voxel-wise level as the coefficient of variation (CoV) across sliding-windows of degree centrality. <h3>Results:</h3> At follow-up, 25/129 (19.3%) MS patients worsened clinically. At baseline, MS patients showed reduced TVFC <i>vs</i> HC in the bilateral orbitofrontal cortex (p<0.05, family-wise error corrected), left cerebellum, right precuneus and left thalamus. At 2.5-year follow-up, a widespread reduction of TVFC over time (p<0.05, family-wise error corrected) was found in MS patients in temporal, parietal, occipital and frontal lobes, as well as in the cerebellum. Such a pattern of TVFC reduction was also found when looking at clinically stable MS patients. Clinically worsened MS presented peculiar TVFC reductions in areas of the default-mode network and basal ganglia. Reduced TVFC in the left putamen in clinically worsened <i>vs</i> stable MS patients was significant at time <i>x</i> group interaction analysis. <h3>Conclusions:</h3> After 2.5 years of follow-up, MS patients showed widespread TVFC reduction in cortical lobes and cerebellum. A peculiar involvement of deep grey matter was found in clinically worsened MS patients. Accrual of TVFC abnormalities in deep grey matter regions may represent a biological substrate of disability worsening. <b>Disclosure:</b> Dr. D’Amore has nothing to disclose. Paola Valsasina has received personal compensation in the range of $500-$4,999 for serving on a Speakers Bureau for ACCMED. Mr. Preziosa has received personal compensation in the range of $500-$4,999 for serving on a Speakers Bureau for Bristol Myers Squibb . Mr. Preziosa has received personal compensation in the range of $500-$4,999 for serving on a Speakers Bureau for Sanofi Genzyme. Mr. Preziosa has received personal compensation in the range of $500-$4,999 for serving on a Speakers Bureau for Novartis. Mr. Preziosa has received personal compensation in the range of $500-$4,999 for serving on a Speakers Bureau for Roche. Mr. Preziosa has received personal compensation in the range of $500-$4,999 for serving on a Speakers Bureau for Merck. Monica Margoni has received research support from MAGNIMS. Dr. Filippi has received personal compensation in the range of $5,000-$9,999 for serving as a Consultant for Bayer, Biogen Idec, Merck-Serono, Novartis, Roche, Sanofi Genzyme, Takeda, and Teva Pharmaceutical Industries. Dr. Filippi has received personal compensation in the range of $5,000-$9,999 for serving on a Speakers Bureau for Bayer, Biogen Idec, Merck-Serono, Novartis, Roche, Sanofi Genzyme, Takeda, and Teva Pharmaceutical Industries. Dr. Filippi has received personal compensation in the range of $5,000-$9,999 for serving as an Editor, Associate Editor, or Editorial Advisory Board Member for Springer Nature. The institution of Dr. Filippi has received research support from Biogen Idec, Merck-Serono, Novartis, Roche, Teva Pharmaceutical Industries, Italian Ministry of Health, Fondazione Italiana Sclerosi Multipla, and ARiSLA (Fondazione Italiana di Ricerca per la SLA). Maria Assunta Rocca has received personal compensation in the range of $500-$4,999 for serving on a Speakers Bureau for Bayer, Biogen, Bristol Myers Squibb, Celgene, Genzyme, Merck Serono, Novartis, Roche, and Teva. The institution of Maria Assunta Rocca has received research support from Italian Ministry of Health, MS Society of Canada and Fondazione Italiana Sclerosi Multipla.