Surrogate-based optimization is employed to maximize the thermo-hydraulic performance of a solar air heater duct with non-periodic rows of rectangular winglet pairs mounted in the absorber plate. The present optimization study encompasses the variation of Reynolds number (5000 and 10,000) and of three geometric parameters for each row of rectangular winglets such as chord of the winglets ranging from 8 mm to 40 mm; height of winglets from 8 mm to 21 mm; and angles of attack from 15 degrees to 45 degrees (Flow-Up) and from -45 degrees to -15 degrees (Flow-Down). The Pareto frontiers show that periodic configurations are suboptimal solutions, i.e., the thermo-hydraulic performance of a solar air heater with rectangular winglet pairs not periodically arranged along the channel outperform the periodic arrangements. The aspect ratios and angles of attack for non-periodic and periodic optimized designs are completely different from each other. Moreover, the optimized solutions for Flow-Down arrangement present higher performance than Flow-Up, and this behavior is independent of the Reynolds number. Complex flow patterns and heat transfer mechanisms of the non-periodic optimized solutions are observed, especially the interactions of corner and main vortices along the duct. The first row of winglet pair play the most important role on pressure penalty and heat transfer enhancement when compared to the other rows of rectangular winglet pairs, mainly on Flow-Up arrangement at Re = 10,000. In general, Flow-Up arrangements create a vortex structure more intense than Flow-Down arrangement.