In this study, we isolated a new sulfonic acid derivative, (Z)-4-methylundeca-1,9-diene-6-sulfonic acid (1), from the sea urchin collected from the Sea of Okhotsk. We established the structure of this new compound by analysis of NMR and HRMS data, along with comparison of the data with those of the related compounds reported in the literature. In addition, we investigated its anti-inflammatory effects in LPS-stimulated RAW264.7 macrophages. Compound 1 inhibited the production of NO, iNOS, $PGE_2$, and COX-2, and it also suppressed the production of proinflammatory cytokines, such as $TNF-{alpha}$ and $IL-1{eta}$. It inhibited the translocation of the $NF-{kappa}B$ subunit p65 into the nucleus by interrupting the phosphorylation and degradation of $I{kappa}B-{alpha}$. In addition, compound 1 significantly decreased the phosphorylation of JNK and p38 in LPS-stimulated RAW264.7 macrophages, suggesting that suppression of the inflammation process by compound 1 was mediated through the MAPK pathway. Taken together, this study showed that the anti-inflammatory effects of a new sulfonic acid derivative, (Z)-4-methylundeca-1,9-diene-6-sulfonic acid were mediated through the inhibition of $NF-{kappa}B$ and JNK/p38 MAPK signaling pathways.