The photosynthetic performance (leaf gas exchange and chlorophyll a (Chla) fluorescence), activities of antioxidant enzymes [superoxide dismutase (SOD), catalase (CAT), peroxidase (POX), ascorbate peroxidase (APX)] and the concentrations of hydrogen peroxide (H2O2) and malondialdehyde (MDA) in the flag leaves of plants from two wheat cultivars with contrasting levels of resistance to spot blotch was assessed. Spot blotch severity was significantly lower in plants from cv. BR-18 compared to cv. Guamirim. Net carbon assimilation rate, stomatal conductance and concentrations of Chla, Chlab and carotenoids were significantly decreased from fungal infection. In contrast, internal CO2 concentration was significantly increased from fungal infection in comparison to their non-inoculated counterparts. Similarly, inoculation significantly reduced photochemical performance in the inoculated flag leaves in comparison to their non-inoculated counterparts. However, plants from cv. BR-18 were able to sustain greater functionality of the photosynthetic apparatus during fungal infection process compared to cv. Guamirim. The activities of SOD, POX, APX and CAT increased in inoculated flag leaves from both cultivars compared to non-inoculated plants, and the highest increases were measured in cv. BR-18. The greater activities of these enzymes were associated with a reduced H2O2 concentration in the inoculated flag leaves from cv. BR-18, resulting, therefore, in a lower MDA concentration. Thus, a more efficient antioxidative system in flag leaves from cv. BR-18 plays a pivotal role in removing the excess reactive oxygen species that were generated during the infection process of Bipolaris sorokiniana, therefore limiting cellular damage and largely preserving the photosynthetic efficiency of the infected flag leaves.