A method based on spatial frequency domain imaging platform and different back-processing algorithms are used together to present the refractive index (RI) of mouse brain tissue in the NIR spectral range. Structured light patterns at two frequencies of six wavelengths ranging between 690 and 970 nm were serially projected onto mouse scalp while a camera mounted above the head captures the reflected diffuse light. In the computer, the recorded images at each wavelength were converted to spatial absorption and scattering maps, respectively. Then, algorithms based on Maxell equations, Hilbert Transform, and Kramers-Kronig relations are used separately to calculate the RI. Once the value of RI at each wavelength was obtained, the wavelength dependence of RI was fitted using four well-known dispersion models. In addition, three-dimensional surface-profile distribution of RI was achieved based on phase profilometry principle. During this study, RI was evaluated in mouse model of heatstress (HS) showing a decrease in RI with increasing wavelength and overall differences pre-and-post HS. An in-house system was built to control the body temperature and thermal camera together with IR laser temperature meter gun was used to measure brain temperature. The changes in RI we observed reflect the pathophysiology of the brain during HS and present an additional advantage of spatial frequency domain imaging technique to characterize brain function. Overall, this work demonstrates a proofof- concept of the proposed method which we believe will be beneficial to the Biophotonics' community.