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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 …