Green microalgae are a recognized lutein source; however, processing for lutein production requires additional operations such as extraction and saponification, mainly due to the high green pigment and lipid content in the biomass. In this study lutein was isolated from a chlorophyll-deficient Parachlorella kessleri HY1 strain using high-performance countercurrent chromatography (HPCCC). The lower phase of the biphasic solvent system composed of n-heptane–ethanol–water, 5:4:1.5, v/v/v was used both as biomass extraction solvent and HPCCC mobile phase conferring a high selectivity to the lutein production process. For the HPCCC isolation, a multiple injection method was developed, and ten consecutive sample injections (300 mg per each) were performed. To favor the economics of the process, the HPCCC mobile and stationary phases were separately formulated based on nuclear magnetic resonance (NMR) analyses. This strategy enabled to avoid obtaining immiscible liquid phases from their parent biphasic solvent system, which led to the reduction of the separation process duration and solvent consumption. Overall, 3 g of P. kessleri HY1 strain extract was processed by HPCCC yielding 150 mg of lutein (95% purity, 97% recovery). The results presented here form an efficient and economical basis for the large-scale production of microalgae-sourced lutein.