R-phycoerythrin (RPE) extracted from the red alga Gracilaria verrucosa by enzymatic hydrolysis generates a large amount of coproduct containing agar. We developed a process for the sequential extraction of RPE and agar. A Box–Behnken design with three factors–three levels and response surface methodology were applied to study the influence of different extraction parameters (incubation temperature, incubation time, and algae-to-water ratio) on the yield, 3,6-anhydrogalatose (3,6-AG) content, and sulfated degree of agar from RPE coproduct. The extraction efficiency was maximized (28%) when the extraction process was carried out with these conditions: incubation temperature of 100 °C, time of 2.6 h, and algae-to-water ratio equal to 3 (% w/v). Optimum 3,6-AG content (30%) was maximized at 85 °C, 1.85 h, and 2.35 (% w/v). Sulfated degree varied between 6 and 12%. The results of this study indicate that fresh G. verrucosa can be subjected to a process of simultaneous extraction of R-phycoerythrin and agar.