Fucoidan from marine algae is used as a functional ingredient in the food. Here, we purified fucoidan fractions from a crude polysaccharide obtained after the crude polysaccharide of celluclast-assisted hydrolysate from Ecklonia cava (ECC). We evaluated the effect of ECC on lipid accumulation in differentiated 3T3-L1 adipocytes and investigated its anti-obesity effects in vivo in high-fat diet (HFD)-induced obese mice. In vitro Oil Red O staining revealed that treatment with ECC and its purified fucoidan fractions of celluclast assisted hydrolysate from Ecklonia cava (ECFs) remarkably reduced lipid accumulation in 3T3-L1 cells. ECF3 contained the highest contents of polysaccharides and sulfate compared with other fucoidan fractions. ECF3 treatment significantly reduced lipid accumulation in 3T3-L1 cells. Oral administration of ECC significantly reduced body weight, body weight gain, serum lipid content, and total white adipose tissue mass. Histological analysis revealed that ECC reduced lipid accumulation in EAT and liver tissues. Our findings suggest that the anti-obesity effects of ECC are associated with suppressing lipid accumulation in white adipose tissues and increased energy expenditure by upregulating the expression of thermogenic UCP1 and UCP3 in BAT. These results indicate that ECC and its ECFs possess anti-obesity properties and can be used in food and nutraceutical industries.