In the past decades, most of the research studies on airfoil shape design and optimization were focused on high Reynolds number airfoils. However, low Reynolds number airfoils have attracted significant attention nowadays due to their vast applications, ranging from micro-aerial vehicles (MAVs) to small-scale unmanned aerial vehicles. For low Reynolds number airfoils, the unsteady effects caused by boundary layer separation cannot be neglected. In this paper, we present an aerodynamic shape optimization framework for low Reynolds number airfoil that we developed based on the unsteady laminar N–S equation and the adjoint method. Finally, using the developed framework, we performed a test case with NACA0012 airfoil as a baseline configuration and the inverse of lift to drag ratio as the cost function. The optimization was carried out at Re = 10,000 and Ma = 0.2. The results demonstrate the effectiveness of the framework.