Narcissism is one of the most fundamental personality traits in which individuals in general population exhibit a large heterogeneity. Despite a surge of interest in examining behavioral characteristics of narcissism in the past decades, the neurobiological substrates underlying narcissism remain poorly understood. Here, we addressed this issue by applying a machine learning approach to decode trait narcissism from whole-brain resting-state functional connectivity (RSFC). Resting-state functional MRI (fMRI) data were acquired for a large sample comprising 155 healthy adults, each of whom was assessed for trait narcissism. Using a linear prediction model, we examined the relationship between whole-brain RSFC and trait narcissism. We demonstrated that the machine-learning model was able to decode individual trait narcissism from RSFC across multiple neural systems, including functional connectivity between and within limbic and prefrontal systems as well as their connectivity with other networks. Key nodes that contributed to the prediction model included the amygdala, prefrontal and anterior cingulate regions that have been linked to trait narcissism. These findings remained robust using different validation procedures. Our findings thus demonstrate that RSFC among multiple neural systems predicts trait narcissism at the individual level.