The present study aims to design a robust adaptive controller employed in the active tuned mass damper (ATMD) system to overcome undesirable vibrations in multistory buildings under seismic excitations. We propose a novel adaptive type-2 neural-fuzzy controller (AT2NF). All system parameters are taken as unknowns. The MLP neural network is used to extract the Jacobian and estimate the structural model; then, the estimated model is applied to the controller online. To tune the control force applied to the ATMD and achieve the control targets, the controller parameters are adaptively trained using the extended Kalman Filter (EKF) and the error back-propagation algorithm. A PID controller is also included in this method to increase the stability and robustness of the adaptive type-2 neural-fuzzy controller against seismic vibrations. An online simple adaptive controller (OSAC) is studied to demonstrate the suggested controller’s superiority. The OSAC is based on adaptive control of the implicit reference model. In this proposed method, the EKF is used to tune the controller parameters online as a novel feature. The uncertainty associated with identifying the mechanical properties of structures, such as mass and stiffness, is one of the primary challenges in the real-time control of structures. This paper investigates how both controllers cope with parametric uncertainties under far-field and near-field seismic excitation. According to numerical results, the AT2NF controller outperforms OSAC in minimizing the dynamic responses of the structure during an earthquake and accomplishing control objectives when the structure’s characteristics change.