Photobiomodulation (PBM) is a promising approach to treat Parkinson’s disease (PD) symptoms in cellular or animal models. Unfortunately, little information is available on the optical parameters playing a role in the light dosimetry during PBM. We conducted a study to determine the effective attenuation coefficient μeff of PD-relevant human deep brain tissues at 671 and 808 nm, using a multichannel fluence rate-meter comprising sub-millimeter isotropic detectors. The first step involved measurements of tissue modifications induced by postmortem situation and tissue storage on rabbit brains. The parameter μeff was measured using various tissue conditions (in vivo, immediately after sacrifice, after six weeks’ storage at −20°C or in 10 % formaldehyde solution) on eight female New Zealand white rabbits. In the second step, fluence rate was measured at various locations of a frozen human deep brain when the deep brain was illuminated from the sphenoidal sinus. The results were processed by an iterative Monte-Carlo algorithm to generate sets of optical parameters, and results collected on rabbit brains were used to extrapolate the μeff value that would be observed in human deep brain tissues in vivo. Under all tissue conditions, the value of μeff at 808 nm was smaller than that at 671 nm. After long-term storage for six weeks at −20°C, μeff decreased, on average by 15 to 25 % at all wavelengths, while it increased by 5 to 15 % at all wavelengths after storage in formaldehyde. Therefore, a reasonable estimate of in vivo human deep brain μeff values at 671 and 808 nm can be obtained by multiplying the data we report by 120 %.