Pressurized liquid extraction (PLE) at room temperature with a laboratory-assembled system was applied for the extraction of gastrodin (GA) and vanillyl alcohol (VA) in Gastrodia elata Blume. The proposed system setup for this current work was simpler as no heating and backpressure regulator was required. Extraction with PLE was carried out dynamically at a flow rate of 1.5 mL/min, at room temperature, under an applied pressure of 10-20 bars with an extraction time of 40-50 min. The extraction efficiencies of the proposed method using 20% aqueous ethanol were compared with heating under reflux using organic solvents such as methanol and ethanol/water (20:80) for different batches of medicinal plant materials. For the determination of GA and VA in G. elata Blume, the extraction efficiencies of PLE at room temperature were observed to be comparable with heating under reflux. The method precision was found to vary from 1.6 to 8.6% (RSD, n = 6) on different days. The marker compounds present in the various medicinal plant extracts were determined by gradient elution HPLC and HPLC/MS/MS. Our work demonstrated the possibility of implementation of PLE at room temperature and the advantages of minimizing the use of organic solvents in the extraction process.