Seaweeds contain many valuable compounds that can be used in the food industry. Carrageenan is a polysaccharide which has been extracted from seaweed for centuries and is used as a texturizer in food and non-food products. However, seaweeds contain compounds other than carrageenan, such as proteins, which could also be extracted. This extraction should be done without compromising the industrial scale carrageenan extraction yield and quality. This study aimed at up-stream protein extraction from red seaweed Eucheuma denticulatum by using of an optimized enzyme-assisted extraction, including of an aqueous/enzymatic treatment followed by alkaline extraction, and then the commercial carrageenan extraction. The protein extraction efficiency of four enzymes was evaluated including Celluclast® 1.5L, Shearzyme® 500 L, Alcalase® 2.4 L FG and Viscozyme® L at a concentration of 0.0, 0.1, 0.2 and 0.4% (w/w). To avoid detrimental effects on carrageenan, all the experiments were performed at pH 7 at room temperature. The results showed that 0.2% w/w Alcalase® or Viscozyme® added individually achieved the highest protein extraction efficiencies (59 and 48%, respectively) at pH 7 and room temperature (p < 0.05). Determination of the most common carrageenan quality parameters indicated that using any of these enzymes had no negative effect on the carrageenan yield and quality.