Disclosed relates to a method and an apparatus for measuring fluorescence polarization FP in a lab-on-a-chip and, more concretely, to a method and an apparatus that measure quantitatively interactions between biomolecules and fluorescently labeled biomaterials and enzyme activities using the measurement of fluorescence polarization FP. The method and the apparatus of the invention provide rapid assays with minute amounts of samples using an automated device compared to conventional methods. Accordingly, the method and the apparatus of the invention can be usefully applied to the measurement of interactions between biomolecules and to the protease assays using a protein substrate.