An apparatus for sensing biomolecules includes: a storage in which a solution containing a target material is received; a sensor configured to sense the target material; and a flow controller connected between the storage and the sensor to supply the solution to the sensor, wherein the flow controller controls a solution flow to supply the solution containing the target material and the solution containing no target material in an alternating manner. According to the apparatus for sensing biomolecules, the sensing device always achieves a sensing offset, and consequently, long-term continuous measurement is enabled, leading to the maximized usage efficiency of the sensor, and the value of quantitative measurement can be obtained with high precision.