BackgroundBipolar disorder (BD) is a serious mental illness. Several studies have shown that brain structure and function changes and the development of BD are associated with age and sex differences. Therefore, we hypothesized that the functional and structural neural circuitry of BD patients would differ according to age. The amygdala and prefrontal cortex (PFC) are play a key role in the emotional and cognitive processing of patients with BD. In this study, we used magnetic resonance imaging (MRI) to examine the structural and functional connectivity within amygdala-PFC neural circuitry in women with BD at different ages.MethodsForty-nine female patients with BD who were aged 13–25 years and 60 age-matched healthy control (HC) individuals, as well as 43 female patients with BD who were aged 26–45 years and 60 age-matched HC individuals underwent resting-state functional MRI (rs-fMRI) and diffusion tensor imaging to examine the structural and functional connectivity within the amygdala-PFC neural circuitry.ResultsWe found abnormalities in the amygdala-PFC functional connectivity in patients aged 13–25 years and significantly different fractional anisotropy (FA) values in patients aged 26–45 compared with the age-matched HCs. The significance of these findings was indicated by corrected p values of less than 0.05 (uncorrected p values less than 0.001).ConclusionsThe findings in this cross-sectional study suggested that abnormalities in the functional connectivity of the amygdala-PFC neural circuitry are related to the pathophysiology of BD in women aged 13–25 years, while changes in the structural integrity of this neural circuitry are associated with the pathophysiology of BD in women aged 26–45 years. Therefore, functional and structural brain alterations may occur at different ages in female patients with BD.Electronic supplementary materialThe online version of this article (10.1186/s12888-018-1732-9) contains supplementary material, which is available to authorized users.