Fucoidans, a polysaccharide present in various brown seaweeds like Sargassum sp., are increasingly recognized for their health benefits as antioxidants and antimicrobials. Microwave assisted deep eutectic solvent (MA-DES) approach for polysaccharides extraction has been popular compared to the traditional since this method presents a more effective and environmentally safe for achieving a substantial fucoidan yield. In this study, Response Surface Methodology (RSM) was employed to optimize the fucoidan extraction by using MA-DES based on four factors including extraction time (5–35 min), temperature (50–90 °C), water content (10–50%) and solid to liquid ratio (1–3 g/50 mL). The results showed that the highest yield of fucoidan obtained from optimization was 10.4% with the optimized extraction condition of 70 °C, 30% water content, 20 min extraction time and 1:25 g/mL solid to liquid ratio with 2 g raw material loading. This study demonstrates that MA-DES is an effective method for improving the yield of fucoidan, offering enhanced efficiency and time-saving benefits. This study also marks a significant advancement in bioprocessing technology, with important implications for human nutrition. By increasing the extraction efficiency of this bioactive compound, the research opens opportunities for developing functional foods and dietary supplements that are healthy and rich in fucoidan. Such innovations are vital for promoting health and nutrition in an increasingly health-conscious society.