This work details the design and characterization of a low-cost, portable and highly sensitive fluorescence detection system intended for use in a compact and disposable point-of-care (POC) device. The detection device leverages time integration to improve the signal to noise ratio (SNR) compared to instantaneous measurements. It also eliminates complicated focusing optics and electronics typically found in bulky and expensive laboratory-scale devices. Characterization was performed by measuring a series of logarithmically scaled dilutions of 1 μm Nile Red fluorescent microspheres immobilized on microscope slides. This approach eliminates assay dependencies and elucidates the actual system performance. A theoretical model that predicts the time-integrated output voltage profile of the sensor was developed; this prediction is useful for evaluating any lens-free fluorescent system based on a set of filters and choice of fluorophore. By relating the fluorophore concentration, system design parameters, and the output voltage, the model matches well with the empirical data and the limit of determination (LOD) for Nile Red is 20 particles. This system provides a sensitive and potentially low-cost device for fluorescent diagnosis in an integrated and compact/miniaturized POC device, lab-on-chip or a table-top reader.