Unusual flow characteristics such as reverse flow, rotating stalls, flow recirculation, and stationary vortexes can induce high dynamic forces and torque variations on the entire system, creating a positive slope in the discharge-head curve. To avoid these problems, the present study investigates the hydrodynamic characteristics of a lab-scale model of a Francis type pump-turbine unit in the transition region. To verify the simulation, its results were compared with those of a laboratory-scale experiment performed over various operating ranges. The differences between the experimental and numerical speed, discharge, and torque factors were compared. The numerical analysis was well-matched the experimental tendencies in the overall operating and transition regions. The reliability of the simulations was within 4%. The unsteady RANS equations in the SAS–SST model were discretized for a detailed analysis of the pressure and internal flow characteristics. Under the runaway condition and low-discharge conditions, the frequency spectra of the pressure fluctuations were remarkable at low-frequency related to the rotating stall and blade passing frequency. These results represent a rotating stall with a frequency propagation of approximately 60% of the rotational speed of the runner. In case of the internal flow field, some blade loading distributions developed a positive shape while others developed a negative shape under the runaway condition. Although a rotating stall formed under the low-discharge condition, the form under this condition differed from that developed under runaway conditions, owing to backflow and the single stall cell. •The unstable S-shaped characteristics in a lab-scale model were studied.•The numerical results were validated in comparison to the experimental data.•The location and rotating speed of stall under the S-curve region were observed.•The unsteady pressure characteristics were analyzed with internal flow field.