Proanthocyanidins (PAs) contribute to the quality factors and health benefits of several Rosaceae fruits. Ume, also known as Japanese apricot (Prunus mume Sieb. Et. Zucc), is one of the most popular fruit trees grown in Japan, and its processed products are employed as a folk remedy in eastern Asian countries. However, the information available regarding the PAs present in the fruit remains limited. In this study, we analyzed the PAs and phenolic acid derivatives present in the fruit of ‘Nnanko,’ the most common cultivar, and found that the flesh tissue of the mature fruit contained levels of PAs similar to those of the hydroxycinnamic acids. The concentration of PAs in the endocarp tissue of the mature fruit was approximately 14 times higher than that of the flesh tissue. We also estimated the chemical structures of the PAs from the flesh and the endocarp by HPLC-ESI-MS/MS. Although 13 kinds of PAs, including 2 monomers, 4 B-type dimers, 3 A-type dimers, 2 B-type trimers, 1 A-type trimer, and 1 B-type tetramer were detected in the flesh, only 2 monomers, 1 B-type dimer, and 2 A-type dimers were detected in the endocarp. All PAs detected in the endocarp were also present in the flesh.