In the Francis turbine, there are gaps between the runner and the stator structure as the labyrinth seals. The flows inside gaps have the complicated flow phenomena; these complicated flows can affect the hydraulic performance and the downstream of the Francis turbine as the leakage flow. Therefore, it is important to investigate the flow characteristics induced by the runner gaps. However, normally the runner gap that has very complicated flow structure is often disregarded by considering the time and cost of the numerical analysis. But, it is necessary to apply all flow structures correctly to confirm the more accurate and reliable flow phenomena. In this study, the flow characteristics of gaps at the hub and shroud of the Francis turbine model runner were investigated with adding the leakage flow in the runner cone. In addition, the internal flow characteristics were compared by considering with and without the runner gaps application. For observing the influence of the leakage flow on the hydraulic performance and flow characteristics, the three-dimensional steady Reynolds-averaged Navier-Stokes analyses were performed using the shear stress transport turbulence model. The efficiency was decreased by applying the runner gaps; and the complicated flow phenomena were captured in the runner gaps.