Nanomedicines based on nanoparticles rely both on the potency of the drug as well as the efficiency of the delivery system, for which particle size plays a crucial role. For the intracellular delivery of small interference RNA (siRNA), lipid-polymer nanoparticle (LPN) hybrid systems constitute a safe and highly effective class of delivery systems. In the present study, we employ a microfluidics method for the manufacturing of spherical siRNA-loaded LPNs for pulmonary delivery with distinct size distributions with average diameters of approximately 70, 110, and 220 nm. We designed an optically clear, inexpensive thiol-ene polymeric microfluidic chip prototype that is compatible with standard ‘soft-lithography’ techniques, allows for replica molding, and is resistant to harsh solvents. By using SPECT/CT in vivo imaging, we show comparable pulmonary clearance patterns of all three differently sized LPN formulations following intratracheal administration. Also, negligible accumulation in the liver was observed.