Abstract Microalgae oil has great potential to address the growing energy demand and dependence on fossil fuels. However, the multilayered cell walls of microalgae hinder efficient extraction and enhanced lipid recovery. In this study, we develop a novel protocol based on near infrared-assisted extraction (NIRAE) technology to extract efficiently total lipids from Scenedesmus obliquus. Under a greener solvent extraction approach, the effect of nine non-polar/polar solvent systems in various ratios on lipid yield was tested, and the results were compared with Soxhlet, Folch, and Bligh–Dyer methods. The highest oil yields were NIRAE 15.43%, and Soxhlet 22.24%, using AcoEt/MeOH (1:2 v/v). For Folch and Bligh–Dyer, 9.11 and 10%, respectively. The optimized NIRAE conditions obtained using response surface methodology (RSM): 43.8 min, solvent/biomass 129.90:1 (m/v), and AcOEt/MeOH 0.57:2.43 (v/v) increased the oil yield significantly to 24.20%. In contrast to conventional methods, the overall optimized NIRAE process satisfied the requirements of a green extraction because of the simple and safe operation, less solvent toxicity, lower extraction time, and solvent and energy consumption.