An apparatus and a system for measuring the thickness of a thin film are provided. The apparatus includes a signal detector, a Fast Fourier Transform (FFT) generator, an Inverse Fast Fourier Transform (IFFT) generator, and a thickness analyzer. The signal detector detects an electric field signal with respect to a reflected light that is reflected from a thin film. The FFT generator performs FFT with respect to the electric field signal to separate a DC component from an AC component of the electric field signal. The IFFT generator receives the separated AC component of the electric field signal, performs IFFT with respect to the AC component, and extracts a phase value of the AC component. The thickness analyzer measures the thickness of the thin film using the extracted phase value.