Identifying additional imaging biomarkers of lifelong premature ejaculation (LPE) may provide valuable insights into understanding the underlying neural mechanisms of this disorder. Forty-six LPE patients and thirty-five healthy controls (HCs) were enrolled in this study. The Percent Amplitude of Fluctuation (PerAF) method was used to assess differences in brain function in LPE patients compared to HCs during the resting-state. Receiver operating characteristic (ROC) analysis was used to investigate the potential biomarkers based on the imaging findings. Correlation analysis was then applied to examine the relationships between the neuroimaging findings and clinical symptoms. We also investigated whether PerAF alterations in LPE patients were associated with specific neurotransmitter systems. Compared to HCs, LPE patients showed increased PerAF in the middle cingulate cortex (MCC), supramarginal gyrus, Rolandic operculum, parahippocampus/hippocampus (ParaHIPP/HIPP) as well as insula; and decreased PerAF in the precuneus, inferior temporal cortex plus occipital cortex. The MCC and ParaHIPP/HIPP exhibited higher classification performance on ROC analysis. Positive correlations were found between the Premature Ejaculation Diagnostic Tool score and PerAF in the insula, and the International Index of Erectile Function score and PerAF in the precuneus. Additionally, altered PerAF in LPE patients correlated significantly with the spatial distribution of dopamine, acetylcholine and epinephrine pathways. Our findings indicate that LPE patients have PerAF-related changes in certain brain regions associated with visual, sensory and/or emotional processing, and reveal that the abnormal control of ejaculatory function may be related to the combined dysregulation of neurotransmitter systems in LPE patients.