Nitrate (NO3−) contamination of groundwater is a worldwide issue that poses great threats to human health due to the use of the groundwater source for drinking water production. Among the available treatment technologies, bioelectrochemical systems (BESs) have emerged as an attractive treatment approach by using a cathode electrode as an electron donor for the reduction of nitrogen-forms (N-forms). In this work, a mathematical model for autotrophic biocathodic denitrification has been developed. This model successfully simulated both the denitrification process and the current demand by the system, allowing to predict and determine energy consumption related to the reduction of N-forms. The autotrophic denitrification model employed reduced electron carriers (mediators) where each denitrification step competes for the same electron pool based on different electron affinities. This approach allowed to model the exchange of electrons between the cathode and the terminal electron acceptors (TEAs) and the competition for electrons between NO3− and nitrite (NO2−). The current demand was modeled considering two different contributions, namely an electrochemical part and the availability of TEAs in the cathodic chamber. The model was successfully calibrated and validated, and it was able to estimate the current demand, therefore allowing for an estimation of the energy consumption of the BES. A sensitivity analysis showed that the maximum NO2− removal rate and the affinity constant of the reduced mediator for NO2− were the key parameters affecting more the removal of total nitrogen in the model. Altogether our model provides a platform to accurately estimate removal efficiency and energy consumption in autotrophic denitrifying biocathodes.