Since the development of messenger RNA (mRNA)-based SARS-CoV-2 (COVID-19) vaccines, there is increased public awareness of the importance of nanoparticles, in this case lipid nanoparticles, to ensure safe delivery of an active compound. To ensure the formation of high-quality nanoparticles with reproducible results, these lipid nanoparticles are assembled with the nucleic acid drug using flow-based devices. Although flow assembly using lipid nanoparticles for nucleic acid delivery is well described in the literature, only a few examples use polymers. This is surprising because the field of polymers for nucleic acid delivery is substantial as hundreds of polymers for nucleic acid delivery have been reported in the literature. In this review, we discuss several aspects of flow-based assembly of nucleic acid-loaded polymer nanoparticles. Initially, we introduce the concept of chip-based or capillary-based systems that can be either used as single-phase or multiphase systems. Initially, researchers have to choose the type of mixing, which can be active or passive. The type of flow, laminar or turbulent, also significantly affects the quality of the nanoparticles. We then present the type of polymers that have so far been assembled with mRNA, small interfering RNA (siRNA) or plasmid DNA (pDNA) using flow devices. We discuss effects such as flow rate, concentration and polymer lengths on the outcome. To conclude, we highlight how flow assembly is an excellent way to generate well-defined nanoparticles including polyplexes in a reproducible manner.