The primary objective of this study is to introduce a novel adaptive fractional order proportional–integral–derivative (FOPID) controller. The adaptive FOPID controller’s parameters are dynamically adjusted in real-time using five distinct multilayer perceptron neural networks. The extended Kalman filter (EKF) is employed to facilitate the parameter-tuning process. A multilayer perceptron neural network, trained using the error Backpropagation algorithm, is employed to identify the structural system and estimate the plant. The real-time estimated Jacobian is applied to the controller to control the model. The stability and robustness of the adaptive interval type-2 fuzzy neural networks controller are enhanced by utilizing the EKF and the feedback error learning strategy for compensator tuning. This improvement increases resilience against estimation errors, seismic disturbances, and unknown nonlinear functions. The primary objective is to address the challenges posed by maximum displacement, acceleration, and drift, as well as the uncertainties arising from variations in stiffness and mass. In order to validate the reliability of the proposed controller, the performance investigation is carried out on an 11-story building equipped with an active tuned mass damper under far and near-field earthquakes. Numerical findings show the remarkable effectiveness of the proposed controllers compared to their predecessors. In addition, it is revealed that the inclusion of the adaptive interval type-2 fuzzy neural networks compensator has increased the performance of the proposed controller and shows significant capabilities in reducing the seismic responses of structures during severe earthquake events.