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Low-level laser therapy (LLLT) has been clinically utilized for many indications in medicine requiring protection from cell/tissue death, stimulation of healing and repair of injuries, pain reduction, swelling and inflammation. Presently, the use of LLLT to treat stroke, traumatic brain injury and cognitive dysfunction are attracting growing interest. Near-infrared light is capable of penetrating into the cerebral cortex, allowing noninvasive treatments to be carried out with few treatment-related adverse events. Optimization of LLLT treatment effect is a crucial issue of this field; however, only a few experimental tests on mice for wavelength selection have been reported. We addressed this issue by low-cost, straightforward and quantitative comparisons on light dosage distribution within visible Chinese human head by Monte Carlo modeling of near-infrared light propagation. Optimized selection in wavelength, beam type and size were given based on comparisons among frequently used setups (i.e., wavelengths: 660, 810 and 980 nm; beam type: Gaussian and flat beam; beam diameter: 2, 4 and 6 cm). This study provided an efficient way for guiding the optimization of LLLT setup and selection on wavelength, beam type and size for clinical brain LLLT.