Purpose: This is an observational, non-invasive study which measures the VEPs of twelve individuals, at baseline, and under the effect of six monochromatic filters used in visual therapy, to understand their effect on neural activity to propose successful treatments. Methods: Monochromatic filters were chosen to represent the visible light spectrum, going from red to violet color, 440.5–731 nm, and light transmittance from 19 to 89.17%. Two of the participants presented accommodative esotropia. The impact of each filter, differences, and similarities among them, were analyzed using non-parametric statistics. Results: There was an increase on the N75 and P100 latency of both eyes and a decrease was on the VEP amplitude. The neurasthenic (violet), omega (blue), and mu (green) filter had the biggest effects on the neural activity. Changes may primarily be attributable to transmittance (%) for blue-violet colors, wavelength (nm) for yellow-red colors, and a combination of both for the green color. No significant VEPs differences were seen in accommodative strabismic patients, which reflects the good integrity and functionality of their visual pathway. Conclusions: Monochromatic filters, influenced the axonal activation and the number of fibers that get connected after stimulating the visual pathway, as well as the time needed for the stimulus to reach the visual cortex and thalamus. Consequently, modulations to the neural activity could be due to the visual and non-visual pathway. Considering the different types of strabismus and amblyopia, and their cortical-visual adaptations, the effect of these wavelengths should be explored in other categories of visual dysfunctions, to understand the neurophysiology underlying the changes on neural activity.