This paper investigates an application of fractional theory for control and state estimation for a class of noncommensurate systems. A single-link flexible manipulator is considered as a representative example of this class of second-order underactuated systems. A fractional model is proposed and validated experimentally. The fractional-order sliding mode control is synthesized using a novel stable fractional surface. A fractional sliding mode observer is designed for state estimation necessary for implementing the control. The proposed method is validated through simulation and experimentation both.