Migraine pathophysiology is not completely understood and is still a matter of ongoing research. However, functional magnetic resonance imaging studies have provided, over the last few decades, notable insights into neuronal mechanisms underlying migraine. Recently, by using an innovative approach based on repetitive trigeminal painful stimulation, researchers have explored pain processing network functional changes associated with migraine and their correlations with specific migraineous clinical features. These functional changes have been demonstrated during different phases of migraine cycle. However, owing to the complexity of its neurobiology, migraine pathophysiology still has many secrets to be discovered.