Ekşikara (Vitis vinifera L.) is a poorly known native Turkish grape cultivar, which is being cultivated for thousands of years for table consumption, raisin, and grape molasses production. The aim of this study was to investigate the phenolic profile of whole berry, skin, and seeds of the cultivar and to determine the effect of harvesting year and altitude of the vineyard location. The grape samples were collected from two vineyards, located at 1000 and 1500 m of altitude in year 2014 while it was collected from 1500 m of altitude in year 2015. In addition to phenolic profile, antioxidant activity, total phenolic, anthocyanin, and tannin contents, and fatty acid profile of seed oil were also analyzed. In this study, anthocyanins, resveratrol, rutin, and isorhamnetin-3-glucoside were mainly found in skin while monomers and dimers of flavan-3-ols were present mainly in the seed. Altitude had a drastic effect on phenolic compounds as well as on the antioxidant activity of whole berry, skin, and seeds.