<p>In today's scenario, as the internet expands at a faster pace, the number of data consumers also increases at an exponential rate. As the range and number of users increased, a change from traditional homogeneous networks to heterogeneous networks is in demand. However, heterogeneous networks' primary focus is to give a higher quality of service criteria to users. Furthermore, in a heterogeneous network enabled by unmanned aerial vehicles, a large number of users and devices are active. In such a diverse environment, intruder nodes may efficiently operate and transmit numerous harmful actions throughout the network. As a result, the network's entire communication is open to many types of security threats. Therefore, to secure the communication, we used the functional encryption scheme, which allows us to protect the data against intrusion attacks. The whole procedure of establishing a functional encryption scheme in unmanned aerial vehicles integrated heterogeneous network is proposed in this study in two phases: the first phase between user equipment and micro base station, and the second phase between micro base station and unmanned aerial vehicles. The proposed approach is validated using the simulation tool namely Automated Validation of Internet Security Protocols and Applications. The outcome of the security validation ensures that the proposed methodology provides the desired security and robustness to the network.</p>