This study analyzed the temporal dynamics of cerebral blood flow (CBF) modulations, during painful stimulation in fibromyalgia syndrome (FMS), using functional transcranial Doppler sonography. Blood flow velocities were recorded bilaterally in the anterior (ACA) and middle (MCA) cerebral arteries of 24 FMS patients and 20 healthy individuals during exposure to painful pressure stimulation. Participants were presented with two stimulation blocks: a) fixed pressure (2.4 kg) and b) stimulation pressure, individually calibrated to produce equal subjective and moderate pain intensity in all participants. A complex pattern of CBF modulations arose, comprising four main components: an anticipatory increase before stimulation onset, an early increase, a transient decrease to baseline or below, and a final increase. Group differences were observed in all components. The anticipatory component only arose in FMS patients, specifically in the ACA. Patients exhibited a greater early CBF increase under the fixed pressure condition, predominantly in the right ACA. A stronger CBF decrease after the early component was observed in patients during the equal pain condition, in the ACA and MCA. Significant associations were found between clinical pain severity and CBF responses in the MCA. The results demonstrate that acute pain processing is associated with a complex pattern of CBF modulation, where FMS patients exhibited alterations in all phases of the response. The aberrances may be ascribed to psychophysiological phenomena, including central nervous nociceptive sensitization and protective-defensive reflex mechanisms. The anticipatory CBF response in patients may relate to various cognitive, emotional, and behavioral mechanisms involved in pain chronification.