Chemically resistant polymer materials are of great interest due to their versatile implementation in a broad range of applications, including the design of robust microfluidic devices. While flow cells, conventionally fabricated by using poly(dimethylsiloxane) (PDMS), are hardly resistant toward organic solvents, fluorinated materials are chemically inert. However, focusing on the latest developments in microfluidic device design via high-resolution additive manufacturing, e.g., based on micro-stereolithography (μSL), only a few resin formulations have been demonstrated suitable for 3D printing chemically resistant polymer objects. Here, we introduce a homemade resin formulation based on 1H,1H,6H,6H-Perfluoro-1,6-hexyl diacrylate (PFHDA) for high-resolution 3D printing utilizing μSL. By investigating the optical dose, the wettability, the resistance toward organic solvents, and the minimal resolution achievable, we fabricate inner structures down to 200 μm. Finally, water-in-oil (W/O) emulsions are generated in a 3D-printed droplet maker with planar microchannel geometry made from the PFHDA-based resin yielding droplets with an average diameter of 271 μm ± 26 μm. The presented material is resistant against commonly used organic solvents including THF, DMF and toluene with a swelling below 1.5% and shows no solvent-induced damage to the micro-printed structure, which makes the PFHDA-based resin a promising base material for several potential applications such as organic synthesis in microreactors.