We study numerically the effects of free surface on a flapping-foil based ocean current energy extractor. A two-dimensional NACA0015 foil, subjected to a coupled pitching and heaving motions, at a fixed Reynolds number of 900, and varied Froude numbers between 0 and 2, is considered. We fix the non-dimensional frequency at f∗ = 0.16 and pitching amplitude at θ0 = 75°. The previous studies suggested that an energy extracting efficiency up to 0.30 could be achieved in a single-phase fluid flow at these specific parameters. In the current study, as the free surface is considered, we report that both the submergence depth and Froude number affect the energy extracting efficiency. As the submergence depth increases from H = 1 to H = 20, for all the Froude numbers considered, the efficiency converges eventually to 33.7%, though slightly higher efficiencies can be observed when both the depth and Froude number are small. At a fixed submergence depth, the efficiency decreases monotonically with the increasing Froude number, which trend is more pronounced when the depth is small, i.e., the foil is very close to the free surface. It is apparently suggested that the free surface plays an unfavorable role in the energy harvesting efficiency, therefore the foil should be deployed with a sufficiently large distance from the free surface, particularly when it operates at high Froude numbers.