The objective of this work was to evaluate the effect of operating conditions and fructans size distribution on the tight Ultrafiltration process for agave fructans fractionation. A mathematical model of limiting mass flux transfer was used to represent the profile of concentrations over time at the outlet of a pilot scale ultrafiltration system. First, a Box-Behnken experimental design was performed for the optimization of the parameters that determine the operating conditions in their respective ranges: temperature, 30–60 °C; transmembrane pressure (TMP), 1–5 bar and feed concentration, 50–150 kg∙m−3, on the separation factor (SF) and permeate flux. Then, the validation of the model for different fructans size distribution was carried out. The results showed that for SF, the quadratic terms of temperature, TMP and feed concentration were the most significant factors. Statistical analysis revealed that the temperature-concentration interaction has a significant effect (p < 0.005) and that the optimal conditions were: 46.81 °C, 3.27 bar and 85.70 kg∙m−3. The optimized parameters were used to validate the hydrodynamic model; the adjustments conclude that the model, although simplified, is capable of correctly reproducing the experimental data of agave fructans fractionation by a tight ultrafiltration pilot unit. The fractionation process is favored at higher proportions of FOS:Fc in native agave fructans.