A recombinant red fluorescent protein, DsRed, was chosen as a model protein to prepare a protein-encapsulated bioaerogel, DsRed-SAG. It was prepared using sol-gel polymerization of tetraethyl orthosilicate (TEOS) with an ionic liquid as the solvent and pore-forming agent. The DsRed-SAG bioaerogel was characterized by Fourier transformation infrared, scanning electron microscopy and Brunauer-Emmett-Teller measurements. It was found that the as-prepared bioaerogel had high porosity, and the silica network exhibited little shrinkage during the drying process. The stability of the bioaerogel was monitored by fluorescence spectroscopy and confirmed by confocal laser scanning microscopy. In addition, the protection of the encapsulated proteins by the silica network was further investigated using the degradation test by a protease. The results indicated that the as-prepared protein was quite stable during formation of the protein-containing wet gel and extraction of the ionic liquid, demonstrating that the new method can be extended to prepare other protein-encapsulated bioaerogels.