In this work, a compact low-cost system designed to detect low amounts of proteins in biological fluids is presented. The system, based on time-gated fluorescence detection principle, is composed by a Single-Photon Avalanche Diode (SPAD) pixel array, a LED excitation light source and a micro-machined reaction chamber coupled to a microfluidic network. A dual-site binding strategy based on DNA aptamers is used for target protein recognition. The microreactor, composed of an array of microwells covered with a transparent membrane, is functionalized with a primary aptamer, while a fluorescent-tagged secondary aptamer is used for the detection. Preliminary measurements demonstrate the feasibility of fluorescence lifetime detection to discriminate between different fluorophores. The detection of human thrombin protein in 300nM concentration is reported as a biological proof of principle of the biosensor.