Ecklonia cava is a common edible brown algae that is plentiful in Jeju Island of Republic of Korea. Polyphenols from E. cava have strong anti-inflammatory activity. However, a large number of the by-products from E. cava processing are discarded. In the present study, to utilize these by-products, we assessed the anti-inflammatory activity of the polyphenol-rich fraction (PRF) from E. cava processing by-product (EPB) in lipopolysaccharide (LPS)-induced RAW264.7 macrophage cells. Four compounds, namely eckol, eckstolonol, dieckol, and phlorofucofuroeckol-A, were isolated and identified from PRF. We found that PRF suppressed the production of nitric oxide (NO), inducible nitric oxide synthase, and cyclooxygenase-2 in the LPS-induced cells. Furthermore, the protective effect of PRF was investigated in vivo in LPS-stimulated inflammation zebrafish model. PRF had a protective effect against LPS-stimulated toxicity in zebrafish embryos. In addition, PRF inhibited LPS-stimulated reactive oxygen species and NO generation. According to the results, PRF isolated from EPB could be used as a beneficial anti-inflammatory agent, instead of discard.