We perform a gyrokinetic study of 3D resonant magnetic perturbation (RMP) field effect on zonal flows in tokamak plasmas. The result indicates that energy-dependent secular radial drift of particles due to the tangential component () of the RMP field induces a further long term algebraic decay of the Rosenbluth–Hinton (1998 Phys. Rev. Lett. 80 724) residual flow expected in an axisymmetric tokamak. This mechanism could be related to an increase of H-mode transition power threshold in the presence of RMP observed in many tokamak experiments.