This study aimed to evaluate the differences of brain connectivity between healthy subjects (HS) and patients with extracranial internal carotid artery (eICA) stenosis before and after carotid endarterectomy (CEA). An exploratory prospective study was designed. The study population consisted of a patient group (PG) of 20 patients with eICA stenosis eligible for CEA, and a control group (CG) of 20 HS, matched for age and sex. The subjects of the PG group underwent Magnetic Resonance Imaging (MRI) for resting-state functional connectivity MRI (rs-fc MRI) analysis within one week from the CEA (pre-CEA) and 12 months following CEA (post-CEA). The CG underwent a single MRI with the same protocol utilized for the PG. Three region-of-interest to region-of-interest (ROI-to-ROI) rs-fc MRI analyses were conducted: analysis 1 to compare pre-CEA PG and CG; analysis 2 to compare pre-CEA PG and post-CEA PG; analysis 3 to compare post-CEA PG and CG. The Functional Network Connectivity multivariate parametric technique was used for statistical analysis, adopting a p-uncorrected (p-unc) < 0.05 as connection threshold, and a cluster level False Discovery Rate corrected p (p-FDR) < 0.05 as cluster threshold. The clusters were defined by using a data-driven hierarchical clustering procedure. Analysis 1 revealed two clusters of reduced interhemispheric connectivity of pre-CEA PG when compared to CG. Analysis 2 and 3 showed no statistically significant differences. Our exploratory analysis suggests that patients with eICA stenosis have reduced interhemispheric connectivity when compared to a matched control group, and this difference was not evident anymore following endarterectomy.