The objective of the present study was to predict column design parameters using mathematical models such as bed depth service time (BDST) and the empty bed residence time (EBRT). The dynamic adsorption/desorption of anthocyanins from blueberry water extracts was conducted on Amberlite FPX-66 resin in a fixed bed column system. Blueberry anthocyanins were extracted with acidified hot water (90 °C) utilizing high power ultrasound. Breakthrough curves were obtained at different bed depths (5, 7.5, 10, 12.5 and 15 cm) and constant flow rate of 4.0 mL/min. Increase in bed height increased both the breakpoint and exhaustion point of the FPX-66 resin. The experimental data fitted well to BDST model at 5% of the breakthrough curve (R2 = 0.9864). The EBRT was in the range of 3.75–10.25 min at different bed depths. In addition, desorption of anthocyanins was studied at different ethanol concentrations and sigmoid equation was applied to obtain maximum recovery rates. Practical Applications Anthocyanins are antioxidant flavonoids in blueberries. They are responsible for the blue color of the berries and are known to promote better health by preventing chronic diseases. A concentrated anthocyanin extract from blueberries has the potential to be used as dietary supplement, natural colorant and functional food ingredient. This present study optimized resin adsorption method to concentrate polyphenols and remove sugars using mathematical models. Optimization of the column design parameters can be used in designing a pilot/industrial scale column for the separation and concentration of anthocyanins from blueberries.