The electromagnet levitation control system (EMS) is the core component of the magnetic levitation train. However, its nature is characterized by an inherent instability and strongly nonlinear dynamic. Additionally, modeling uncertainties and numerous exogenous perturbations make the design of the controller even more difficult for this system. To overcome these limitations, a Fuzzy Sliding Mode Control based on Interval Type-2 Fuzzy Neural Network Identification (FSMCF2NN) is designed for the EMS system. The suggested controller has a unique feature that allows the sliding surface and controller effort to be designed by using model-free techniques. As a result, the drawbacks of the conventional SMC schemes, such as the chattering effect, requiring prior knowledge of the system’s uncertainties bounds, and selection of the appropriate control gains, are eliminated. Also, the FSMCF2NN method, since it is designed based on intelligence methods not only minimizes the accumulation of state errors, but also generates the optimum control efforts of the EMS system to ensure stability in different situations. Furthermore, since the measurement of all EMS states is not achievable in reality, a qualified observer is needed to estimate unmeasured states. For this purpose, the Extended Kalman-Bucy filter (EKBF) is selected because of its superiority in managing disturbances for nonlinear systems. Furthermore, to confirm the robustness of the FSMCF2NN scheme in different scenarios, the results of the controller based on Linear Matrix Inequality (LMI), Linear Quadratic Regulation (LQR) controller, and the conventional Sliding Mode Controller (SMC) are compared with the proposed controller. Analyzing the results of simulation demonstrates that maintaining the levitated object is achievable with the proposed control scheme, effectively. At the same time, it attempts to adequately compensate for the uncertainties and disturbances present in the EMS structure.