In this study, the human-induced dynamic performance of modern footbridges equipped with either classical reinforced concrete (RC) or innovative glass fiber-reinforced polymer (GFRP) composite deck slabs were investigated and compared. The numerical studies were carried out for two bridges: a three-span cable-stayed footbridge and a three-span continuous beam structure. Two variants of both bridges were taken into consideration: the footbridges equipped with traditional RC slabs and the structures benefitted with GFRP slabs. The risk of resonance as well as the vibration serviceability and the comfort criteria assessment of the footbridges with different slab materials were assessed. The investigation revealed that the footbridges, both cable-stayed and beam, benefitted with the GFRP slabs had higher fundamental frequency than those with the traditional RC slabs. The footbridges with the GFRP slabs were less exposed to the resonance risk, having fundamental frequencies above the limit of the high risk of resonance. The effect of shifting up the natural frequencies by introducing GFRP slabs was more remarkable for the lightweight beam structure than for the cable-stayed footbridge and resulted in a more significant reduction of the resonance risk. The calculated maximum human-induced accelerations of the footbridges benefitted with the GFRP slabs were meaningfully higher than those obtained for the footbridges with the RC slabs. The study proved that, with the same GFRP slab, meeting vibration serviceability and comfort criteria limits in the case of very lightweight beam structures may be more problematic than for cable-stayed footbridges with more massive structural systems. In the research, particular attention was paid to examining the impact of higher harmonics of the moving pedestrian force on the structures benefitted with the GFRP composite slabs. It occurred that in the case of footbridges, both cable-stayed and beam, equipped with the RC slabs higher harmonics of human force did not play any role in the dynamic performance of structures. However, in the case of the footbridges benefitted with the GFRP slabs, the impact of higher harmonics of the pedestrian force on the dynamic behavior of structures was clearly visible. Higher harmonics excited accelerations comparable to those executed by the first harmonic component. This conclusion is of great importance for footbridges equipped with GFRP slabs. The fundamental frequency may place a footbridge in the low or even negligible risk resonance range and the higher frequencies corresponding to vertical modes may be located above the limit of 5 Hz that ensures avoiding resonance. Nevertheless, the fact that fundamental modes are so responsive to higher harmonics significantly increases the risk of resonance. The amplification of the dynamic response may occur due to frequencies related to second or third harmonics (i.e., being half or a third of the natural frequencies). In such cases, full dynamic analysis of a footbridge at the design stage seems to be of crucial importance.