Affective processing, including induction and regulation of emotion, activates neural networks, induces physiological responses, and generates subjective experience. Dysregulation of these processes can lead to maladaptive behavior and even psychiatric morbidity. Multimodal studies of emotion thus not only help elucidate the nature of emotion, but also contribute to important clinical insights. In the present study, we compared the induction (EI) and effortful regulation (ER) with reappraisal of fear and disgust in healthy subjects using functional near infrared spectroscopy (fNIRS) in conjunction with electrodermal activity (EDA). During EI, there was significant activation in medial prefrontal cortex (PFC) for fear and more widespread activation for disgust, with right lateral PFC significantly more active during disgust compared to fear. ER was equally effective for fear and disgust reducing subjective emotion rating by roughly 45%. Compared to baseline, there was no increased PFC activity for fear during ER, while for disgust lateral PFC was significantly more active. Significant differences between the two negative emotions were also observed in sympathetic nerve activity as reflected in EDA during EI, but not during ER. Lastly, compared to men, women had higher emotion rating for both fear and disgust without corresponding differences in EDA. In conclusion, in the present study we show that emotion induction was associated with differential activation in both PFC and sympathetic nerve activity for fear and disgust. These differences were however less prominent during emotion regulation. We discuss the potential interpretation of our results and their implications regarding our understanding of negative emotion processing.