Aquaponic facilities allow the joint production of fish and plants in a reduced space. This hydroponic technique, combined with vertical farming, is not well studied. The main objective of this work was to compare basil production between horizontal and vertical decoupled aquaponic systems and assess the utilization of supplemental lighting in a greenhouse environment. Six independent vertical racks were arranged with hydroponic trays at three heights. Three racks were affixed with LED lighting on the lowest levels and three with supplemental lighting on the intermediate level. Immediately adjacent to the vertical systems, two independent horizontal systems containing three trays were constructed to compare basil production. After 35 days of growth post transplanting, the total production per tray and weight, height, number of leaves, and nodes of 20 selected plants per tray were determined. Records of the intensity of illumination photosynthetic photon flux density (PPFD)) were recorded at dawn (8:00), noon (12:00), and dusk (18:00) at randomly predetermined positions associated with the 20 selected plants per tray. The total basil production in the experiment was 58.79 kg, with an average production per unit area of 2.43 and 0.94 kg m−2 for vertical and horizontal systems, respectively. Productivity per unit area in the vertical systems was 160% greater than in horizontal systems. A significant effect of lighting, the height of the tray, and plant position inside the tray was found on plant growth parameters. Optimization of light source distribution and tray orientation can enhance the productive performance in vertical aquaponic systems. Electricity cost associated with supplemental lighting per kg of production increment was 21.84 and 12.25 $ kg−1 for the bottom and intermediate levels of the vertical system, respectively, the latter being economically the most profitable.