We study effects of eccentricity fluctuations on the elliptic flow coefficient v_2 at mid-rapidity in both Au+Au and Cu+Cu collisions at sqrt{s_{NN}}=200 GeV by using a hybrid model that combines ideal hydrodynamics for space-time evolution of the quark gluon plasma phase and a hadronic transport model for the hadronic matter. We find that the effect of eccentricity fluctuation is modest in semicentral Au+Au collisions but significantly enhances v_2 in Cu+Cu collisions.