Pistacia lentiscus L. is a Mediterranean shrub known for its health promoting effects attributed to a large extent to polyphenols accumulated in all parts of the plant. Microwave-assisted extraction is a green extraction technique enabling fast and effective isolation of plant polyphenols. Therefore, the aim of this research was to optimize the microwave-assisted extraction of polyphenols from Pistacia lentiscus L. leaves and fruit in terms of temperature, extraction time and microwave power and to evaluate their polyphenolic profile by UPLC/ESI-MS2 and antioxidant capacity by ORAC assay. Optimal extraction conditions for leaf polyphenols were 69 °C, 512 W and 12 min, while for fruit were slightly more intensive—75 °C, 602 W and 15 min. Obtained total phenolic content in leaves and fruit was similar to that obtained after 30 min of the heat-reflux method. The polyphenolic profile of extracts included 34 compounds, with myricetin glycosides being the most abundant compounds among flavonoids in Pistacia lentiscus L. leaves and fruit and gallic acid and its derivates among the phenolic acids. ORAC assay showed higher antioxidant capacity for Pistacia lentiscus L. leaves extract than for fruit, which is in correlation with their respective phenolic content.