In this study, we investigated the potential antioxidant abilities of low-molecular weight fucoidans from enzyme-assisted hydrolysates of Sargassum autumnale, based on molecular weight changes, in vitro and in vivo. The yield and free radical-scavenging activities of enzyme-assisted hydrolysates of S. autumnale were screened. The protamex-assisted hydrolysate of S. autumnale (SAP) presented the highest yield and 2,2-diphenyl-1-picrylhydrazyl (DPPH)-scavenging activity; therefore, it was chosen for fucoidan purification. Three fucoidan fractions were observed in SAP, and their antioxidant activity was assessed. Fucoidan fraction 3 of protamex-assisted hydrolysate of S. autumnale (SAPF3) offered significant protection against H2O2-induced oxidative stress, and was structurally and physically similar to commercial fucoidan. Fucose and low-molecular weight fucoidans were highly concentrated in SAPF3. The results of our study show that SAPF3, a low-molecular weight fucoidan from S. autumnale, possesses strong antioxidant properties and may be an effective alternative to antioxidant agents in the functional food industry.