Phytanic acid is one of the branched‐chain fatty acids in the human diet. Humans incorporate it into their bodies through the ingestion of ruminant meat and milk since these animal products contain the 3RS, 7R, 11R‐isomer, as naturally occurring phytanic acid (nPA). Although phytanic acid has been reported to have health‐promoting effects such as immunomodulatory effects, these findings were obtained mostly from in vitro cell‐based experiments. In this study, the in vivo anti‐inflammatory effects of nPA were investigated using a mouse model of dextran sulfate sodium (DSS)‐induced colitis. Mice were fed diets containing 0%, 0.05%, or 0.1% nPA for 4 weeks. During the fourth week, acute colitis was induced by administration of a 3% DSS solution. The intake of 0.05% and 0.1% nPA inhibited DSS‐induced body weight loss in mice, and showed improvement of histopathological changes in colon epithelium. nPA also inhibited the production of proinflammatory cytokines, especially macrophage‐related cytokines such as interleukin‐1β in the colon. These results suggest that nPA exerts anti‐inflammatory effects under in vivo physiological conditions.Practical application: There is a growing demand for fatty acids possessing distinct nutritional and physical characteristics in the realms of health, nutrition, and food‐related applications. The present study demonstrated that a branched‐chain fatty acid, phytanic acid, exerts anti‐inflammatory activity under not only in vitro but also in vivo conditions, using a commonly used mouse model of human inflammatory bowel disease. Our findings encourage further studies to determine whether phytanic acid elicits beneficial properties in humans, and suggest that phytanic acid enrichment can be a novel product strategy in the food market.