The aim of this work was to isolate and investigate subcortical and cortical lateral interactions involved in flicker perception. We quantified the perceived flicker strength (PFS) in the center of a test stimulus which was simultaneously modulated with a surround stimulus (50% Michelson contrast in both stimuli). Subjects were requested to adjust the modulation depth of a separate matching stimulus that was physically identical to the center of the test stimulus but without the surround. Using LCD goggles, synchronized to the frame rate of a CRT screen, the center and surround could be presented monoptically or dichoptically. In the monoptic condition, center-surround interactions can have both subcortical and cortical origins. In the dichoptic condition, center-surround interactions cannot occur in the retina and the LGN, therefore isolating a cortical mechanism. Results revealed both a strong monoptic (subcortical plus cortical) lateral interaction and a weaker dichoptic (cortical) lateral interaction. Subtraction of the dichoptic from the monoptic data revealed a subcortical mechanism of the lateral interaction. While the modulation of the cortical PFS component showed a low-pass temporal-frequency tuning, the modulation of the subcortical PFS component was maximal at 6 Hz. These findings are consistent with two separate temporal channels influencing the monoptic PFS, each with distinct lateral interactions strength and frequency tuning characteristics. We conclude that both subcortical and cortical lateral interactions modulate flicker perception.