The pressure fluctuation caused by unsteady flow in runner is one of the main reasons of vibration for a large Francis hydraulic turbine. It directly affects the steady operation of the hydraulic turbine unit. The existing research of the pressure fluctuation in hydraulic turbine mainly focuses on the unsteady flow in draft tube. Accurate distribution of pressure fluctuations inside a runner is not very clear. In this paper, the numerical method for predicting the pressure fluctuations in runner is investigated and the numerical simulation is performed for a large Francis hydraulic turbine. It is proved that the combination of shear-stress transport(SST) k-w turbulence model and pressure-implicit with splitting of operators(PISO) algorithm could give more reliable prediction of pressure fluctuations in runner. The frequencies of pressure fluctuations in runner are affected by the flow in guide vane and the flow in draft tube. The first dominant frequency is significantly determined by the flow in draft tube, especially at part load condition. This frequency is approximately equal to one-third of the runner rotating frequency. The evident second dominant frequency is exactly equal to the guide vane passing frequency. The peak-to-peak amplitudes of pressure fluctuations in runner at small guide vane open angle are larger than that at large open angle at the same operating head. The amplitudes at points on blade pressure surface are generally greater than that on suction surface. The research results could be used to direct the hydraulic design and operation stability improvement of a large Francis hydraulic turbine. The pressure fluctuation caused by unsteady flow in runner is one of the main reasons of vibration for a large Francis hydraulic turbine. It exists affects the steady operation of the hydraulic turbine unit. The existing research of the pressure fluctuation in hydraulic turbine mainly focuses on the unsteady flow in draft tube. Accurate distribution of pressure fluctuations inside a runner is not very clear. In this paper, the numerical method for investigating the pressure fluctuations in runner is investigated and the numerical simulation is performed for a large Francis hydraulic turbine. It is proved that the combination of shear-stress transport (SST) kw turbulence model and pressure-implicit with splitting of operators (PISO) algorithm could give more reliable prediction of pressure fluctuations in runner. The frequencies of pressure fluctuations in runner are affected by the flow in guide vane and the flow in draft tube. The first dominant frequency is significantly determined by the flow in draft tube, especially at part load condition. This frequency is approximately equal to one-third of the runner rotating frequency. The evident second dominant frequency is exactly equal to the guide vane passing frequency. pressure fluctuations in runner at small guide vane open angle are larger than that at large open angle at the same operating head. The amplitudes at points on blade pressure surface are generally greater than that on suction surface. The research results could be used to direct the hydraulic design and operation stability improvement of a large Francis hydraulic turbine.