Pressurized liquid extraction (PLE) has been used for the first time in this work to extract phenolic compounds from Goji berries according to a multilevel factorial design using response surface methodology. The global yield (% w/dw, weight/dry‐weight), total phenolic content (TPC), total flavonoid (TF) and antioxidant activity (determined via ABTS assay, expressed as TEAC value) were used as response variables to study the effects of temperature (50–180°C) and green solvent composition (mixtures of ethanol/water). Phenolic compounds characterization was performed by high performance liquid chromatography–diode array detector–tandem mass spectrometry (HPLC‐DAD‐MS/MS). The optimum PLE conditions predicted by the model were as follows: 180°C and 86% ethanol in water with a good desirability value of 0.815. The predicted conditions were confirmed experimentally and once the experimental design was validated for commercial fruit samples, the PLE extraction of phenolic compounds from three different varieties of fruit samples (Selvatico mongolo, Bigol, and Polonia) was performed. Nine phenolic compounds were tentatively identified in these extracts, including phenolic acids and their derivatives, and flavonols. The optimized PLE conditions were compared to a conventional solid‐liquid extraction, demonstrating that PLE is a useful alternative to extract phenolic compounds from Goji berry.