This paper presents a zero-dimensional dynamic model of redox flow batteries (RFBs) for the system-level analysis of energy loss. The model is used to simulate multi-cell systems considering the effect of design and operational parameters on energy loss and overall performance. The effect and contribution of stack losses (e.g., overpotential and crossover losses) and system losses (e.g., shunt currents and pumps) to total energy loss are examined. The model is tested by using literature data from a vanadium RFB energy storage. The results show that four parameters mainly affect RFB system performance: manifold diameter, stack current, cell standard potential, and internal resistance. A reduction in manifold diameter from 60 mm to 20 mm reduced shunt current loss by a factor of four without significantly increasing pumping loss, thus boosting round-trip efficiency (RTE) by 10%. The increase in stack current at a low flow rate increases power, while the cell standard potential and internal resistance play a crucial role in influencing both power and energy output. In summary, the modeling activities enabled the understanding of critical aspects of RFB systems, thereby serving as tools for system design and operation awareness.