The fructan separation from a model sugar solution and natural agave juice was studied using a stirred-cell nanofiltration unit operated in concentration mode. Hydrophilic cellulose membrane with MWCO of 1000Da was used. The experimental conditions were varied to predict the influence of pressure (0.14-0.350MPa) and feed concentration (0.15-0.25g/mL) on the initial permeate flux and solute retained fraction (SRF) values of the process. Response surface plots (p<0.05) showed that the permeate flux and SRF increased significantly with the pressure and decreased with feed concentration. The permeate flux varied from 0.5 to 4.1Lh(-1)m(-2). The fructan retained fraction in model sugar solution varied from 0.85 to 0.97 whereas fructose, glucose and sucrose presented similar SRF values ranging from 0.38 to 0.65. Promising results were obtained when natural agave juice was used.