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This research assesses the brain activity and visual performance at baseline and after light therapy (LTH), of seventeen patients with strabismus and amblyopia (SA), and eleven healthy controls (HCs) from Querétaro, México. Quantitative electroencephalogram analysis (qEEG) was used to record the brain activity, and clinical metrics such as the visual acuity, angle of deviation, phoria state, stereopsis, and visual fields determined the visual performance. Results showed a constant higher alpha-wave frequency for HCs. Low voltages remained negative for HCs and positive for SA patients across stimulation. After LTH, high voltage increased in SA patients, and decreased in HCs. A second spectral peak, (theta-wave), was exclusively recorded in SA patients, at baseline and after LTH. Positive Spearman correlations for alpha-wave frequency, low and high voltages were only seen in SA patients. Synchronized brain activity was recorded in all SA patients stimulated with filters transmitting light in the blue but not in the red spectrum. Enhancement in the visual performance of SA patients was found, whereas deterioration of the phoria state and a decrease in the amount of stereopsis was seen in HCs. To conclude, only a suffering brain and a visual pathway which needs to be enabled can benefit from LTH. [ABSTRACT FROM AUTHOR]