To produce polymer optical fibers in research environments, a flexible cladding material-application process is required. Further, to functionalize the waveguide, the fiber core-production step needs to be separated from the cladding application, contrasting conventional polymer optical fiber production processes. In this study, we developed a solution using continuous dip-coating technique to apply cladding material onto previously extruded polymer optical fiber cores with diameters as low as 16 µm. The process was designed considering the fluid-dynamic behavior of the cladding material and fiber to achieve a radially symmetric coating thickness. We examined UV-curable resin as cladding and polymethyl-methacrylate (PMMA)-based extruded optical fibers with diameters of up to 16 µm. The proposed method helped continuously coat optical fiber cores with cladding material with diameters in the range of 1 mm and achieve the lowest optical attenuation (<3 dB/m).