Precise control of a variable geometry turbocharger (VGT) is critical to fuel economy, efficiency and emission performance of the engine. This paper describes physical nonlinear modeling and control of a commercial pneumatic actuator used in the VGT system. This model incorporates friction and aerodynamic force related effects, such as hysteresis, using adaptive LuGre model. In order to compensate for parametric uncertainties, two novel nonlinear position control laws are designed for the single-input single-output system using the second order sliding mode (SMC) and backstepping control methods. A comparative study with experimental results shows the effectiveness of the proposed controllers.