In search for new biologically active compounds, several new fluorine‐substituted pyrimido [2,3‐c][1,2,4]triazino (3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16) have been synthesized via the nucleophilic attack of 2‐hydrazinopyrimidinone (2) toward more positive carbons under different conditions. Structure of the newly synthesized compounds was deduced from elemental analyses as well as their spectral data (UV, IR, NMR, and M/S). The antifungal activity of the target ring systems has been evaluated both in vitro and in vivo against some phytopathogenic fungi associated with wheat grains. Result showed that compounds 6, 7, and 8 have high protection of wheat grains against the fungal infection.