The notable medical efficacy of 3,6-anhydrogalactose (called “AHG” hereafter), the usefulness of galactose (called “GA” hereafter) as a biofuel source, and the need to utilize renewable resources have led to a significant increase in an interest in the economical productions of AHG and GA from agarose in marine red algae. One of the major challenges for realizing AHG and GA productions in this way has been to establish a highly efficient and reliable process for recoveries of both AHG and GA from the hydrolysates of agarose, which, however, has not been attempted so far. To address such issue, this study aimed to develop an optimal simulated-moving-bed (SMB) process for the continuous-mode and high-purity recoveries of AHG and GA from agarose hydrolysates. It was found first that a two-stage SMB structure based on using a less hydrophobic adsorbent in the 1st-stage SMB and a more hydrophobic adsorbent in the 2nd-stage SMB was most appropriate for the targeted SMB process. Under the environment of such selected SMB adsorbents, the intrinsic parameters of each component were determined, which were then applied to the optimization of the targeted SMB process. The simulations for such optimized process demonstrated that the front and rear of each solute wave were completely trapped within its corresponding zones in the optimized process, thereby enabling the SMB separation goal to be attained as designed. Finally, it was confirmed from the SMB experimental results that the optimized process allowed the continuous-mode recoveries of AHG and GA without loss, while maintaining 100% purities. Therefore, the developed SMB process in this study is expected to promote the economical productions of AHG and GA based on the utilization of agarose in marine red algae.