A method of detecting a biomolecule, a computing device performing the method, and a biomolecule detection system therefor are provided. The method includes receiving a terahertz signal that passed deionized water or reference material, receiving a terahertz signal that passed a target including a predetermined biomolecule, extracting a digital modulation characteristic for the received terahertz signal that passed the deionized water and the received terahertz signal that passed the target, and detecting the predetermined biomolecule included in the target by analyzing the extracted digital modulation characteristic, wherein the received terahertz signal that passed the deionized water and the received terahertz signal that passed the target are generated using a digitally modulated optical signal based on a transmission speed determined based on kinematics of the predetermined biomolecule.