In this article, a new intelligent hybrid controller is proposed. The controller is based on the combination of the orthogonal endocrine neural network (OENN) and orthogonal endocrine ANFIS (OEANFIS). The orthogonal part of the controller consists of Chebyshev orthogonal functions, which are used because of their recursive property, computational simplicity, and accuracy in nonlinear approximations. Artificial endocrine influence on the controller is achieved by introducing excitatory and inhibitory glands to the OENN part of the structure, in the form of postsynaptic potentials. These potentials provide a network with the capability of additional self-regulation in the presence of external disturbances. The intelligent structure is trained using a developed learning algorithm, which consists of both offline and online learning procedures: online learning for fitting OENN substructure and offline learning for adjusting OEANFIS parameters. The learning process is expanded by introducing the learning rate adaptation algorithm, which bases its calculations on the sign of the error difference. Finally, the proposed intelligent controller was experimentally tested for control of a nonlinear multiple-input-multiple-output two rotor aerodynamical system. During the test phase, an additional four related intelligent control logics and default PID-based controllers were used, and tracking performance comparisons were performed. The proposed controller showed notably better online results in comparison to other control algorithms. The major deficiencies of the structure are complexity and noticeably large training computation time, but these drawbacks can be neglected if tracking performances of a dynamical system are of the highest importance.