In this study, the preparation of an inclusion complex of baicalein (BAI) and hydroxypropyl-β-cyclodextrin (HP-β-CD) using the precipitation with compressed antisolvents (PCA) process was studied. The goal was to improve the solubility, antioxidant activity, antibacterial activity and bioavailability of BAI, an active component in traditional herbal medicines. DSC, XRD, and SEM results confirmed the formation of an inclusion complex between BAI and HP-β-CD. The solubility of BAI in the BAI/HP-β-CD inclusion complex improved remarkably. A relatively high BAI solubility of 147.38 μg/mL was reported in the inclusion complex (particle size = 0.295 μm) formed under the following conditions (pressure = 14 MPa, temperature = 318 K, mole ratio of BAI/HP-β-CD = 1:2). Both in vitro and in vivo study, proved the bioavailability enhancement of BAI by a supercritical antisolvent process via coprecipitation with HP-β-CD. After efficient complexation using the PCA process, the limited antioxidant activity and antibacterial activity of BAI was highly enhanced together with the aqueous solubility. Hence, this study provides valuable information for the potential clinical application of inclusion complexes of BAI using the PCA process.