Even though lifelong premature ejaculation (PE) is highly prevalent, few studies have investigated the neural mechanisms underlying PE. The extent and pattern of brain activation can be determined through a version of functional magnetic resonance imaging (fMRI) with erotic picture stimuli (task fMRI) and a resting-state fMRI (rs fMRI). We showed that the brain activity in the left inferior frontal gyrus and left insula was decreased both during the task and in the resting state, while there was higher activation in the right middle temporal gyrus during the task. Higher functional connectivity was found in PE between those three brain areas and the bilateral middle cingulate cortex, right middle frontal gyrus and supplementary motor area. Moreover, the brain activity had positive correlation with clinical rating scales, such as intravaginal ejaculatory latency time (IELT) and the Chinese Index of Premature Ejaculation (CIPE). These findings revealed that brain responses and functional integration in certain brain areas are impaired in cases of PE, which was consistently supported by multiple measurements obtained using a task and rs fMRI approach.