A general picture of refractive index change mechanisms in glass modified by a femtosecond laser has proven elusive. In this paper, Raman microscopy was used in conjunction with refractive near-field profilometry to analyse the structure of borosilicate glass (Schott BK7) modified by a femtosecond laser and determine the mechanism of the observed refractive index change. For a pulse repetition rate of 1 kHz, it was determined that the refractive index change was due to an elevated population of non-bridging oxygen atoms, resulting in more ionic bonds forming within the glass network and increasing the molar refractivity of the glass. For a pulse repetition rate of 5.1 MHz, the dominant mechanism of refractive index change was densification and rarefaction of the glass network. Different refractive index change mechanisms were attributed to different thermal conditions imparted to the glass under different pulse repetition rates. Implications for device fabrication are also discussed. These findings constitute an important step toward a complete overview of femtosecond-laser-induced refractive index change in glass. Waveguides were fabricated in BK7 glass using femtosecond laser pulses and subsequently investigated using Raman microscopy. It was determined that for waveguides written at a 1 kHz pulse repetition rate, refractive index change correlated with the formation of B-O- groups, whereas for waveguides written at a 5.1 MHz repetition rate, refractive index change correlated with changes in density of the glass. The mechanism behind these structural changes and the implications on device fabrication are discussed.