Very little is known about the physiological interactions between wheat quality and Fusarium head blight (FHB), which substantially reduces wheat grain yield and quality worldwide. In order to investigate stress-induced changes in flag leaves from plants artificially inoculated with Fusarium, we screened for chlorophyll a fluorescence transient at 1, 2, 4, 7 and 14 days after Fusarium inoculation. Our results indicate that the maximum quantum yield of photochemistry (Fv/Fm) and the performance index (PI) were not affected by FHB, but there were significant differences in those two traits between different varieties and measurement times. FHB caused a significant reduction in the percentage of glutenins (GLU), high-molecular-weight (HMW), and low-molecular-weight (LMW) subunits in ‘Kraljica’ and ‘Golubica’, unlike ‘Vulkan’, where the percentage of GLU increased.