Peptide nucleic acids (PNAs) are charge-neutral oligonucleotides with emerging potential for treatment of genetic, acquired, and viral diseases, including COVID-19. Their challenging synthesis, however, limits their use for rapid therapeutic intervention and widespread application. Here, we report a highly efficient technology that utilizes a fully automated fast-flow instrument to manufacture cell-penetrating peptide-conjugated PNAs (PPNAs) in a single shot. The machine is rapid: each amide bond is formed in 10 seconds and the synthesis of an 18-mer bioactive PNA is complete in one hour. Anti-IVS2-654 PPNA synthesized in a single shot with this instrument presented over 16-fold activity compared to unmodified PNA in a splice-correction assay. We demonstrated the utility of this approach by chemically synthesizing an eight-member anti-SARS-CoV-2 PPNA library within one day. A designer PPNA targeting the 5’ untranslated region of SARS-CoV-2 genomic RNA reduced the viral titer by over 95% in live virus infection assays (IC50: 0.8 mM). Our technology can rapidly yield on-demand PPNA candidates to tackle newly-emerging viral pathogens.