Vranac, an old autochthonous red grapevine variety of Montenegro, was first mentioned in a historical document published in the 15th century. As currently the study of indigenous varieties is of particular importance, the subject of this work was detailed characterization of phenolic compounds in the autochthonous grapevine variety Vranac, from the Montenegrin Podgorica subregion. Phenolic profiles of leaves, berries (skin, seeds, and pulp were examined separately) and young monovarietal wine were determined using ultra-high performance liquid chromatography (UHPLC) with linear trap quadrupole (LTQ)—Orbitrap XL mass spectrometry (MS). Total phenolic content (TPC) and radical scavenging activity (RSA) were higher for the grape seeds extracts, followed by extracts of grape skins and pulps. As expected, the total anthocyanin content (TAC) was higher in grape skin than in wine. A total of one hundred twenty nine compounds (forty two phenolic acids and their derivatives, twenty three flavan-3-ols, twenty one flavanols, five stilbenes and thirty eight anthocyanins) were identified in the investigated extracts. To our best knowledge, this is the first report of tentative identification of (epi)catechin 3-O-coumarate in grape seed and chalcan-flavan 3-ol dimers in wine and grape seed.