The aviation industry needs led to an increase in the number of aircraft in the sky. When the number of flights within an airspace increases, the chance of a mid-air collision increases. Systems such as the Traffic Alert and Collision Avoidance System (TCAS) and Airborne Collision Avoidance System (ACAS) are currently used to alert pilots for potential mid-air collisions. The TCAS and the ACAS use algorithms to perform Aircraft Trajectory Predictions (ATPs) to detect potential conflicts between aircrafts. In this paper, three different aircraft trajectory prediction algorithms named Deep Neural Network (DNN), Random Forest (RF) and Extreme Gradient Boosting were implemented and evaluated in terms of their accuracy and robustness to predict the future aircraft heading. These algorithms were as well evaluated in the case of adversarial samples. Adversarial training is applied as defense method in order to increase the robustness of ATPs algorithms against the adversarial samples. Results showed that, comparing the three algorithm’s performance, the extreme gradient boosting algorithm was the most robust against adversarial samples and adversarial training may benefit the robustness of the algorithms against lower intense adversarial samples. The contributions of this paper concern the evaluation of different aircraft trajectory prediction algorithms, the exploration of the effects of adversarial attacks, and the effect of the defense against adversarial samples with low perturbation compared to no defense mechanism.