The velocity profile of backflow in a hybrid aligned nematic (HAN) liquid crystal cell is experimentally and numerically analyzed to investigate the effect of initial molecular configuration on the backflow. The HAN cell is achieved by coupling two kinds of surface anchoring treatments which are planar and homeotropic anchoring treatments, and generates the molecular orientation profile varying continuously from homeotropic orientation at the bottom surface to planar orientation at the upper surface. The velocity profile of the backflow is experimentally visualized by tracing small particles mixed in the liquid crystal and is also numerically solved using the Leslie-Ericksen continuum theory. It is found from the results that there are two stages with different time scales of the backflow development. One is the rapid increase of the flow just after application of an electric field, and the other is the transition of the backflow profile. The rapid increase occurs in the time scale of several microseconds, whereas the transition occurs in several tens of milliseconds. Since the HAN cell creates the backflow effectively, it must be useful for the liquid crystal applications, such as liquid crystalline actuators.