Balanus rostratus is a large cold-water acorn barnacle distributed around the northern coast of the Pacific Ocean. In Mutsu Bay, Aomori, Japan, B. rostratus, which adhere naturally to scallop shells, are cultured as food. However, current culture methods do not generate sufficient supplies to satisfy market demand. Knowledge of the physiology of B. rostratus reproduction is important for the development of more efficient aquaculture methods. Previous studies have suggested that fatty acids and their metabolites play an important role in barnacle reproduction and development; however, few studies have analyzed lipids, particularly during ovary maturation. Here we analyzed lipid content, lipid class, and fatty acid composition of B. rostratus ovary throughout the year. The clutch in the present study was observed once per year at the end of November. The lipid content increased as the ovary underwent maturation. The proportion of triacylglycerol increased with increasing lipid content. The proportions of myristic acid, arachidonic acid, EPA and DHA significantly decreased in December. By contrast, the proportion of these fatty acids in lipid extracted from larvae was high relative to lipid extracted from B. rostratus ovary in December. These findings suggest that these fatty acids are transferred from the ovary to the larvae. Our novel findings on lipid metabolism during ovary maturation in B. rostratus indicate the importance of lipids during reproduction. This information may be useful in establishing methods for the aquaculture of B. rostratus.