Oligonucleotides have attracted the widespread attention in disease diagnosis and gene therapy. At present, the nucleic acid drugs are at the forefront of biomedical and pharmaceutical research. The bioanalysis of therapeutic oligonucleotides has been slow, however, due to the requirements for pharmacokinetic/toxicokinetic and pharmacodynamic studies in pharmaceutical development. Conventionally, the hybridization-enzyme linked immunosorbent assay (hybridization-ELISA) is widely used in the bioanalysis of therapeutic oligonucleotides. Recentlly, many technologies such as real-time quantitative PCR (qPCR) and high performance liquid chromatography (HPLC)-based technologies have also showed a broad application prospects in the bioanalysis of therapeutic oligonucleotides. However, each technology has its own advantages and limitations. This review summarizes the currently used techniques in the bioanalysis of oligonucleotide therapeutics and reviews the challenges of regulated bioanalysis.