Protection of high-yielding winter wheat (WW) with fungicides increases the productivity of nitrogen (N) present in the soil–crop system during the growing season. As a consequence of the action of fungicides, the nitrogen gap (NG) reduces. This hypothesis was verified on the basis of data from a field experiment conducted with WW during three growing seasons (2013/2014; 2014/2015, 2015/2016) in Poland. The field experiment included two crop protection systems (CP): (i) CP-0—without fungicides and CP-F—with fungicides and (ii) six N doses increased gradually by 40 kg N ha⁻¹ from 0 to 240 kg N ha⁻¹. The grain yield (GY) of WW treated with fungicides was significantly higher than that of the unprotected. The difference in yields between both CP systems was 17.3% on a plot fertilized with 200 kg N ha⁻¹ (9.13 vs. 11.2 t ha⁻¹). The fungicide yield gap increased progressively with N_f doses from 0.76 t ha⁻¹ in the N_f control plot to 2.17 t ha⁻¹ in the fertilized with 200 kg ha⁻¹. The use of fungicides increased the amount of N in grain (N_gr) from 15 kg N ha⁻¹ in the control N plot to 51 kg N ha⁻¹ in the plot with 200 kg N ha⁻¹. The main source of additional N in grain (N_gr) was inorganic N released from the soil (N_g89) during the WW growing season. The maximum N_g89 values were 64.4 and 83.0 kg N ha⁻¹. These values corresponded to N_f doses of 94.4 and 80.8 kg N ha⁻¹. The N_g89 of 70.1 kg N ha⁻¹ conditioned 100-percentage N_f recovery. As a consequence, the prediction reliability of GY and N_gr was highest when N_g89 was used as a predictor. The net increase in the absolute NG size in response to increasing N input was significantly slower and therefore smaller in fungicide-protected than in unprotected WW. It can be concluded that the use of fungicides due to the increase in inorganic N productivity in the soil–crop system reduces the potential threat of N dispersion into the environment. In the light of the results obtained, it should be concluded that the fungicidal protection of crop plants should be treated as a factor significantly reducing the nitrogen gap and, thus, the yield gap.