Sea buckthorn (Hippophae Rhamnoides L.) is an important source of bioactive compounds such as: antioxidants, vitamins, fatty acids, amino acids, and minerals. Sea buckthorn leaves extracts have been proved to have anti-microbial, antioxidant, anti-inflammatory, and anti-viral properties. In this paper, the extraction of polyphenols from sea buckthorn leaves using a semi-continuous small-scale reactor is described. The extraction conditions must not affect the composition and structure of polyphenols. For this reason, the influence of different parameters (residence time, solvent flow rate, stirring rate, reactor type, and solvent pre-heating) on the extraction process were studied. The polyphenolic extracts were analyzed in order to determine the total phenolic content (TPC), the antioxidant capacity and the concentration of the main phenolic compounds. The TPC increases with the stirring rate. Pre-heating the solvent leads to a better yield and reduced residence time. The antioxidant capacity is in concordance with the TPC results. HPLC analysis confirms that the semi-continuous microwave assisted extraction (MAE) does not affect the composition of the extracts. The energy consumption was significantly lower for MAE compared with conventional extraction (CE).