We report the effect of high‐repetition rate femtosecond (fs) laser irradiation on structure‐terahertz (THz) property relationship for sodium borosilicate glasses. We have used nuclear magnetic resonance (NMR), terahertz time‐domain spectroscopy (THz‐TDS), and Raman spectroscopy to examine pristine and laser irradiated regions of these glasses to determine and quantify boron speciation, THz refractive index, n(THz), and change (Δn) in n(THz), and spectral, that is, structural, changes due to laser exposure, respectively. Our results suggest that laser irradiation‐induced Δn(THz) values are dependent upon the glass composition, structural units, connectivity, and network, for example, the corresponding K‐ and R‐values of the borosilicate glass. Depolymerized glass networks show no changes in NMR B4 signal, slight changes in Raman spectral changes related to silicate structural units, for example, increase in Q3 tetrahedra with one nonbridging oxygen (nbO) atom, and higher measurable n(THz) and Δn(THz). More polymerized glasses, on the other hand, show changes in NMR B4 signal, varying degrees of Raman spectral changes in the borate subnetwork and structural units, and lower n(THz) and Δn(THz). The THz refractive index is most sensitive to modifier ions in the glasses, which are directly responsible for nbO formation, glass structure, and network polymerization.