Introduction: In this study, we investigated whether abnormalities of the brain resting-state networks (RSNs) occur in patients with episodic cluster headache (CH), outside the attacks of the disease. Patients and methods: RS fMRI scans were acquired from 13 CH patients and 15 healthy controls. RS fMRI data were analyzed using both independent component analysis (ICA) and a seed correlation analysis, starting from the hypothalamus and the thalamus. Results: The seed correlation analysis revealed increased functional connectivity within the networks identified starting from the hypothalami and thalami in CH patients versus controls. ICA analysis detected 11 RSNs with potential functional relevance. Among these networks, CH patients had decreased fluctuations within the sensorimotor and the primary visual network compared to controls ( P-values 0.03–0.007). RSN abnormalities were significantly correlated with disease duration. Conclusions: In CH patients a diffuse abnormality of brain functional connectivity is present, which extends beyond the antinoceptive system.