We have developed an aptameric enzyme subunit (AES) for protein sensing. AES is composed of an enzyme-inhibiting aptamer and a target molecule-binding aptamer and it can allosterically control the corresponding enzyme activity by binding target molecules. Here, we applied AES to immunoglobulin E (IgE) sensing. We split the thrombin-inhibiting aptamer into two oligonucleotides and then connected IgE-binding aptamer and its complementary strand to the split thrombin-inhibiting aptamer. The hybrid of these two oligonucleotides inhibited thrombin enzymatic activity and it was decreased in the presence of IgE. We were able to detect IgE by using the AES in homogeneous assay and detection limit was 250 nM.