Bioelectronic medicine is an emerging approach to treat many types of diseases via electrical stimulation of the autonomic nervous system (ANS). Because the vagus nerve (VN) is one of the most important nerves controlling several ANS functions, stimulation protocols based on knowledge of the functional organization of the VN are particularly interesting. Here, we proposed a method to localize different physiological VN functions by exploiting electro-neurographic signals recorded during spontaneous VN fibers activity. We tested our method on a realistic human cervical VN model geometry implanted via epineural or intraneural electrodes. We considered in silico ground truth scenarios of functional topography generated via different functional neural fibers activities covered by background noise. Our method accurately estimated the underlying functional VN topography by outperforming state-of-the-art methods. Our work paves the way for development of spatially selective stimulation protocols targeting multiple VN bodily functions.