Electrification of the field of transport is one of the key elements needed to reach the targets of greenhouse gas emissions reduction and carbon neutrality planned by the European Green Deal. In the railway sector, the hybrid powertrain solution (diesel–electric) is emerging, especially for non-electrified lines. Electric components, especially battery power systems, need an efficient thermal management system that guarantees the batteries will work within specific temperature ranges and a thermal uniformity between the modules. Therefore, a hydronic balancing needs to be realized between the parallel branches that supply the battery modules, which is often realized by introducing pressure losses in the system. In this paper, a thermal management system for battery modules (BTMS) of a hybrid train has been studied experimentally, to analyze the flow rates in each branch and the pressure losses. Since many branches of this system are built inside the battery box of the hybrid train, flow rate measurements have been conducted by means of an ultrasonic clamp-on flow sensor because of its minimal invasiveness and its ability to be quickly installed without modifying the system layout. Experimental data of flow rate and pressure drop have then been used to validate a lumped parameter model of the system, realized in the Simcenter AMESim® environment. This tool has then been used to find the hydronic balancing condition among all the battery modules; two solutions have been proposed, and a comparison in terms of overall power saved due to the reduction in pressure losses has been performed.