Field effect transistors (FETs) based on networks of randomly oriented Si nanowires (Si nanonets or Si NNs) were biomodified using Thrombin Binding Aptamer (TBA–15) probe with the final objective to sense thrombin by electrical detection. In this work, the impact of the biomodification on the electrical properties of the Si NN–FETs was studied. First, the results that were obtained for the optimization of the (3-Glycidyloxypropyl)trimethoxysilane (GOPS)-based biofunctionalization process by using UV radiation are reported. The biofunctionalized devices were analyzed by atomic force microscopy (AFM) and scanning transmission electron microscopy (STEM), proving that TBA–15 probes were properly grafted on the surface of the devices, and by means of epifluorescence microscopy it was possible to demonstrate that the UV-assisted GOPS-based functionalization notably improves the homogeneity of the surface DNA distribution. Later, the electrical characteristics of 80 devices were analyzed before and after the biofunctionalization process, indicating that the results are highly dependent on the experimental protocol. We found that the TBA–15 hybridization capacity with its complementary strand is time dependent and that the transfer characteristics of the Si NN–FETs obtained after the TBA–15 probe grafting are also time dependent. These results help to elucidate and define the experimental precautions that must be taken into account to fabricate reproducible devices.