Genetic analysis in microfluidic devices commonly relies on detection of fluorescence intensity from dyes bound to DNA fragments. Aim of this work was to develop an experimental setup and a method for obtaining fluorescence intensity of liquids placed in microfluidic chips by analyzing digital fluorescence images under light excitation. This article describes an experimental setup for detection of fluorescence signal from sample placed into reaction chamber of microfluidic chips with a 25 × 40 mm field of view. The system directs excitation radiation from an LED (λavg = 480 nm, P = 3 W, Umax = 6 V, Imax = 0.6 A) through a bandpass filter (467–498 nm) and a lens onto the surface of a microfluidic chip. The selected parameters of the system enable efficient excitation of fluorescent dyes without overlapping their emission spectrum. Experiments were performed using fluorescein isothiocyanate solutions of different concentrations. Comparison of the signal-to-noise ratio values of the presented experimental setup with that of a commercially available realtime polymerase chain reaction device (ANK-48) has been carried out. The key advantages of the proposed system are its ability to perform full-area fluorescence detection on the microfluidic chip and its flexibility in terms of chip topology, i. e., the ability to work using chips of various designs and geometries.