This paper presents a physics-guided deep neural network framework to estimate fuel consumption of an aircraft. The framework aims to improve data-driven models' consistency in flight regimes that are not covered by data. In particular, we guide the neural network with the equations that represent fuel flow dynamics. In addition to the empirical error, we embed this physical knowledge as several extra loss terms. Results show that our proposed model accomplishes correct predictions on the labeled test set, as well as assuring physical consistency in unseen flight regimes. The results indicate that our model, while being applicable to the aircraft's complete flight envelope, yields lower fuel consumption error measures compared to the model-based approaches and other supervised learning techniques utilizing the same training data sets. In addition, our deep learning model produces fuel consumption trends similar to the BADA4 aircraft performance model, which is widely utilized in real-world operations, in unseen and untrained flight regimes. In contrast, the other supervised learning techniques fail to produce meaningful results. Overall, the proposed methodology enhances the explainability of data-driven models without deteriorating accuracy.