The antisense phosphorodiamidate morpholino oligomer (PMO) drugs Eteplirsen and Golodirsen are improving the lives of some Duchenne muscular dystrophy (DMD) patients, but treating all DMD subtypes would require the development of over 50 novel antisense therapies. To rapidly prototype personalized PMO for diseases such as DMD, we designed a fully automated flow-based oligonucleotide synthesizer. Our optimized high temperature synthesis platform reduces coupling times by up to 22-fold compared to previously reported batch methods. We demonstrate the power of our new automated technology with the synthesis of milligram quantities of an 18-mer reporter PMO sequence in 3.5 hours, three new potential therapeutic PMO sequences targeted to exon 46 of the dystrophin gene in a single day, and a candidate antiviral PMO sequence targeted to the SARS-CoV-2 genomic mRNA in 3.5 hours. This flexible flow synthesis platform can be used for on-demand production of a broad range of personalized therapeutic polymers.