Suitable and accurate flow measurement in pumped storage hydropower plants (PSP) is a challenging task due to the entirely different hydraulic behaviour of the penstock. This study presents a novel approach to choosing a suitable flow measurement method and position. The focus is on the flow measurement in a specific short penstock of the largest peak-load hydropower plant, Orlík, after its transformation to a PSP. Our approach is based on three main pillars: numerical modelling of fluid flow (ANSYS CFX), standards, and scientific literature. First, the steady-state numerical model output for the current state is compared to historical measurements of point velocities using current meters and measured hydraulic losses in the penstock. Subsequently, for the planned conversion to the reversible Francis turbine, including shape modifications of the flow paths, a steady numerical simulation of the flow in the penstock was performed in both turbine and pump modes. By analysing the resulting pressure and velocity fields and comparing them to standards and scientific literature, the values of the uncertainty in the flow measurement were calculated. The outcome is a straightforward evaluation and comparison of three main flow measurement methods: current meter, pressure–time, and ultrasonic transit time.