Fluorozirconate glasses, such as ZBLAN (ZrF4-BaF2-LaF3- AlF3-NaF), have a high infrared transparency and large rare-earth solubility, which makes them an attractive platform for highly efficient and compact mid-IR waveguide lasers. We investigate the structural changes within the glass network induced by high repetition rate femtosecond laser pulses and reveal the origin of the observed decrease in refractive index by using Raman microscopy. The high repetition rate pulse train causes local melting followed by rapid quenching of the glass network. This results in breaking of bridging bonds between neighboring zirconium fluoride polyhedra and as the glass resolidifies, a larger fraction of single bridging fluorine bonds relative to double bridging links are formed in comparison to the pristine glass. The distance between adjacent zirconium cations is larger for single bridging than double bridging links and consequently an expansion of the glass network occurs. The rarified glass network can be related to the experimentally observed decrease in refractive index via the Lorentz-Lorenz equation.