The global trend toward renewable power generation has drawn great attention to hydrogen Fuel Cells (FCs), which have a wide variety of applications, from utility power stations to laptops. The Multi-stack Fuel Cell System (MFCS), which is an assembly of FC stacks, can be a remedy for obstacles in high-power applications. However, the output voltage of FC stacks varies dramatically under variable load conditions; hence, in order for MFCS to be efficiently operated and guarantee an appropriate load-current sharing among the FC stacks, advanced converter controllers for power conditioning need to be designed. An accurate circuit model is essential for controller design, which accounts for the fact that the parameters of some converter components may change due to aging and repetitive stress in long-term operations. Existing control frameworks and parametric and non-parametric system identification techniques do not consider the aforementioned challenges. Thus, this paper investigates the potential of a data-driven method that, without system identification, directly implements control on paralleled converters using raw data. Based on pre-collected input/output trajectories, a non-parametric representation of the overall circuit is produced for implementing predictive control. To achieve proper current sharing, the proposed method considers also the mitigation of circulating current within the MFCS. Simulation results verify the effectiveness of the proposed method.