The Internet of Drones (IoD) is a network paradigm where drones will fly over well-defined airways. The Jamming Attack (JA) poses a severe risk to IoD, affecting the drone’s trajectory. Although JA has been investigated in UAV-based networks, the current solutions consider the airspace free to fly, whereas IoD allows drones to fly over constrained airspace, named airways. This study investigates the impact of JA over IoD, mainly regarding the drone path planning and, therefore, the drone trajectory. Also, we conduct a thorough discussion regarding the current challenges. To overcome these challenges, we propose the IoD-JAPM, an airway-aware protection mechanism against JA on the IoD, ranging from analyzing the airway’s availability to the potential reformulation of the drone path planning. We perform an experimental evaluation through simulations to compare IoD-JAPM with a baseline solution and an existing approach that considers the airspace free to fly, varying the IoD topology and the number of jammers in the environment. We analyze four different metrics to measure at what level IoD-JAPM can mitigate a JA. Through the results, we observe a relation between the impact of JA on the drone path planning and the robustness of the topology, where the more restricted the topology, the more impact JA causes. Also, IoD-JAPM mitigates the effects of JA on path planning, causing few reformulations or even flight cancellations. Specifically, IoD-JAPM prevents all drones from being attacked when the environment has one jammer and mitigates the attack at 30% for two jammers. Furthermore, IoD-JAPM overcomes the baseline study regarding the increasing drone flight distance, and power consumption. Since the drone propellers affect most of the drone battery, the more the flight distance the more the power consumption. Also, the results reinforce that “free-to-fly” approaches cannot be applied in airway-oriented environments with strong jamming signals. In a nutshell, IoD-JAPM represents a robust protection mechanism against JA considering the aerial space defined through airways, advancing the state of the art of IoD-based protection mechanisms against JA.