Nucleic acid aptamers selected for thrombin binding have previously been shown to possess anticoagulant activity, however problems with rapid renal clearance and short circulation half-life prevented translation to clinical usefulness. Here, we describe a family of self-folding, functional RNA origami molecules bearing multiple thrombin-binding RNA aptamers and showing significantly improved anticoagulant activity. These constructs may overcome earlier problems preventing clinical use of nucleic acid anticoagulants. RNA origami structures were designed in silico and produced by in vitro transcription from DNA templates. Incorporation of 2'-fluoro-modified C-and U-nucleotides was shown to increase nuclease resistance and stability during long-term storage. We demonstrate specific binding to human thrombin as well as high stability in the presence of RNase A and in human plasma, comparatively more stable than DNA. The RNA origami constructs show anticoagulant activity seven-fold greater than free aptamer and higher than previous DNA weave tiles decorated with DNA aptamers. Anticoagulation activity was maintained after at least three months of storage in buffer at 4°C. Additionally, inhibition of thrombin is shown to be reversed by addition of single-stranded DNA antidotes. This project paves the way for development of RNA origami for potential therapeutic applications especially as a safer surgical anticoagulant.