Design a nonlinear controller for second order nonlinear uncertain dynamical systems (e.g., internal combustion engine) is one of the most important challenging works. This paper focuses on the comparative study between two important nonlinear controllers namely; computed torque controller (CTC) and sliding mode controller (SMC) and applied to internal combustion (IC) engine in presence of uncertainties. In order to provide high performance nonlinear methodology, sliding mode controller and computed torque controller are selected. Pure SMC and CTC can be used to control of partly known nonlinear dynamic parameters of IC engine. Pure sliding mode controller and computed torque controller have difficulty in handling unstructured model uncertainties. To solve this problem applied linear error-based tuning method to sliding mode controller and computed torque controller for adjusting the sliding surface gain (λ ) and linear inner loop gain (K). Since the sliding surface gain (λ) and linear inner loop gain (K) are adjusted by linear error-based tuning method. In this research new λ and new K are obtained by the previous λ and K multiple gains updating factor(α). The results demonstrate that the error-based linear SMC and CTC are model-based controllers which works well in certain and uncertain system. These controllers have acceptable performance in presence of uncertainty.