Grid-stiffened composite (GSC) structures have been maturely developed in aerospace, aircraft and automobile industries due to their attractive properties such as high specific strength and stiffness, superior load bearing capacity, and excellent energy absorption capability. These structures undergo various loading conditions in service. In the present study, iso-GSC structures reinforced with silica nanoparticles (SiO2) have been investigated in terms of their capability to improve the mechanical properties during transverse loading. At first, a silane coupling agent (3-glycidoxypropyltrimethoxysilane/3-GPTS) was introduced onto the silica nanoparticle surface and the effects of silica content (0, 1, 3, and 5 wt.% with respect to the matrix material) on the three-point flexural response of isogrid E-glass/epoxy composites were assessed. Based on the Fourier transform infrared (FT-IR) spectra, it was inferred that the 3-GPTS coupling agent was successfully grafted onto the surface of silica nanoparticles after modification. The results showed that nano-SiO2 particles incorporation affected the flexural properties of the isogrid fibrous composites. Maximum improvements in the flexural load and energy absorption were obtained after adding 3 wt.% nano-SiO2 particles. In this condition, up to 14% and 25% increase in the maximum flexural load and energy absorption, respectively were observed, compared to the sample without silica addition. In these structures, a considerable amount of energy absorption occurred beyond primary failure at the peak load point. Furthermore, the flexural stiffness was increased by increasing the silica loading. In conclusion, this study suggests that the addition of modified silica nanoparticles is a promising method to improve the flexural properties of the grid-stiffened fibrous composite structures.