A specific analytical procedure including sample preparation and HPLC analysis was developed and validated for the detection of phenolic compounds in the samples of different apples from popular Lithuanian cultivars “Aldas,” “Auksis,” “Ligol,” and “Šampion.” The conditions for phenol extraction were optimized: the solvent of the extraction was 70% (v/v) ethanol, and the extraction was performed in an ultrasound bath for 20 min at the temperature of 40°C. The HPLC mobile phase consisted of 2% (v/v) acetic acid in water and 100% (v/v) acetonitrile. Using the HPLC technique, 11 analytes were identified, and their specificity was confirmed: procyanidin B1, (+)-catechin, chlorogenic acid, procyanidin B2, (−)-epicatechin, rutin, hyperoside, isoquercitrin, avicularin, quercitrin, and phloridzin. Chlorogenic acid was the major component in “Aldas,” “Auksis,” and “Ligol” and procyanidin B2 in “Šampion.” Hyperoside and avicularin were the dominant compounds of all the identified quercetin derivatives in “Aldas” and “Auksis;” hyperoside in “Šampion;” and quercitrin in “Ligol.” The total content of phenolic compounds varied from 1641.0 ± 47.9 μg/g (cv. “Ligol”) to 4291.3 ± 154.2 μg/g (cv. “Aldas”).