Subtilisin Carlsberg was covalently modified with comb-shaped poly(ethylene glycol) (PM13). PM13-modified subtilisin (PM13-Sub) was readily solubilized in three different ionic liquids (ILs), i.e., [Emim][Tf2N], [C2OC1mim][Tf2N] and [C2OHmim][Tf2N]. Analysis of homogeneous enzymatic reactions in the ILs revealed that PM13-Sub exhibited excellent catalytic performance while the native enzyme suspended in ILs showed no activity. Hydrophobicity of ILs slightly affected enzyme activity, and the relatively hydrophobic IL [Emim][Tf2N] was the preferred medium for enzymatic reactions, similar to enzymatic reactions in conventional organic solvents. Enzyme activity was much higher in [Emim][Tf2N] than in conventional organic solvents, and excellent activity was associated with unique properties of ILs such as hydrophobicity and high polarity. Furthermore, PM13-Sub showed good stability in [Emim][Tf2N], and maintained 80% of its initial activity after 60 h.