In this paper, we propose a novel Interval Type-2 (IT2) Fuzzy Cognitive Map (FCM)-based flight control system to solve the altitude, attitude and position control problems of quadcopters. The proposed IT2-FCM encompasses all concepts related to drone for a satisfactory path-tracking and stabilizing control performance. The degree of mutual influences of the concepts is designed with opinions of three experts that take account the dynamics of drone and rules governing proportional integral derivative (PID) controllers. To model the inter-uncertainty of the experts' opinions, IT2 fuzzy logic systems are utilized as they are powerful tools to model high level of uncertainties. Thus, the proposed IT2-FCM has a qualitative representation as it merges the advantages of IT2 fuzzy logic systems and FCMs. We present comparative simulations results in presence of uncertainties where the superiority of the proposed IT2-FCM-based flight control system is shown in comparison with its type-1 fuzzy counterpart.