Sensory stimulation elicits sensations in the phantom hand of individuals with upper limb amputation. The reinstated sensory information is important to improve phantom limb perception and motor performance. In this work, we aimed to characterize the cortical impact of sensory stimulation on sensorimotor integration in upper limb amputees. To this goal, we investigated dynamic functional connectivity computed from electroencephalogram (EEG) recorded while amputees executed phantom hand movements with and without sensory stimulation. We focused on the dynamic functional connections to the somatosensory system and discovered that non-invasive sensory stimulation induced increased speed of information transfer, shown by decreased temporal distance, and increased number of connections from the motor, somatosensory, and multisensory processing systems. We show that the cortical impact of sensory stimulation is manifested not only through functional activities related to the primary somatosensory system, but also those involving the secondary somatosensory system.