This research has been conducted to study extraction of an anionic dye, Alizarin Red S (ARS), from the aqueous phase into the organic phase in a T-junction microchannel. The organic phase included Aliquat 336 and 1-octanol. Equal volumetric flow rates of aqueous and organic phases were adjusted in all the experiments. Designing the experiments and analyzing of the parameters that affect the extraction percentage of ARS were carried out using response surface methodology. The parameters were feed pH, feed concentration, extractant concentration and flow rate of aqueous and organic phases. The maximum extraction percentage of 98.7 was obtained at the feed pH of 3, feed concentration of 5000 mg L−1, extractant concentration of 4 vol.% and flow rate of 2.5 mL min−1. Under the optimum conditions obtained from the experimental design analysis, ARS extraction was performed in a batch system, too. The two-phase contact times to reach the extraction percentage of 98.7 in the microchannel and batch system were 2.4 s and 5.5 min, respectively.