The nanoprecipitation method was used to formulate ε-polycaprolactone (PCL) into fluorescent nanoparticles. Two methods of mixing the phases were evaluated: introducing the organic phase into the aqueous phase dropwise and via a specially designed microfluidic device. As a result of the nanoprecipitation process, fluorescein-loaded nanoparticles (NPs) with a mean diameter of 127 ± 3 nm and polydispersity index (PDI) of 0.180 ± 0.009 were obtained. The profiles of dye release were determined in vitro using dialysis membrane tubing, and the results showed a controlled release of the dye from NPs. In addition, the cytotoxicity of the NPs was assessed using an MTT assay. The PCL NPs were shown to be safe and non-toxic to L929 and MG63 cells. The results of the present study have revealed that PCL NPs represent a promising system for developing new drug delivery systems.