The comprehensive identification of phenolic compounds in food and beverages is a crucial starting point for assessing their biological, nutritional, and technological properties. Pomegranate (Punica granatum L.) has been described as a rich source of (poly)phenolic components, with a broad array of different structures (phenolic acids, flavonoids, and hydrolyzable tannins) and a quick, high throughput, and accurate screening of its complete profile is still lacking. In the present work, a method for UHPLC separation and linear ion trap mass spectrometric (MSⁿ) characterization of pomegranate juice phenolic fraction was optimized by comparing several different analytical conditions. The best solutions for phenolic acids, anthocyanins, flavonoids, and ellagitannins have been delineated and more than 70 compounds have been identified and fully characterized in less than one hour total analysis time. Twenty-one compounds were tentatively detected for the first time in pomegranate juice. The proposed fingerprinting approach could be easily translated to other plant derived food extracts and beverages containing a wide array of phytochemical compounds.