The present study aimed to prepare a chemically and physically stable formulation of baicalein (Ba) in an in situ thermally sensitive hydrogel for vaginal administration. An inclusion complex of Ba and hydroxypropyl-γ-cyclodextrin (HP-γ-CD) was first developed to increase the stability and solubility of Ba in an aqueous solution. The formation of the Ba-HP-γ-CD complex was characterized by scanning electron microscopy (SEM), differential scanning calorimetry (DSC), and X-ray powder diffractometry (XRPD). Poloxamers 407, 188 (P407, P188), sodium alginate (SA), hydroxypropylmethylcellulose (HPMC), and benzalkonium bromide were mixed to obtain a hydrogel with an appropriate gelation temperature for vaginal use. Among the formulations examined, P407/Ba-HP-γ-CD/HPMC/P188/benzalkonium bromide (18/0.96/0.5/4.0/0.02%) represented the appropriate gelation temperature and acceptable drug release rate at the administration site. Release of Ba-HP-γ-CD from the poloxamer hydrogel followed Peppas equation, which suggests that it occurred through coupled corrosion-diffusion mechanism, and the corrosion-release curve showed that corrosion was the primary mode of release. In animal study, treatment by using Ba-HP-γ-CD thermosensitive hydrogel could produce a restoration of damaged tissues. Thermosensitive hydrogel formulation of the Ba-HP-γ-CD complex appears to be a promising treatment for cervicitis.