Biobanks may transfer biological materials and personal data to third countries when they process or use collected biological materials and personal data. Taiwan’s Human Biobank Management Act pays close attention to and strictly regulates transborder flows. Yet, interpreting and applying the provisions encounters a couple of thorny questions. Moreover, it is difficult to find the rationale behind the provisions if we compare the provisions with the related international development. The purpose of this paper is to seek potential answers to the questions regarding the interpretation and application of the provisions and provide the direction for the future legal reform. This paper argues that the regulation over the transborder flows of biological materials and data of biobanks under the Human Biobank Management Act probably has gone beyond the necessary limit to pursue the end of the regulation and should be reconsidered by the legislature. As for the interpretation and application of the current provisions, this paper suggests that the subject matter of the review and permit of the competent agency could be interpreted as the whole scheme of a biobank for addressing transborder transfers. This interpretation makes the provisions relatively consistent with the end of the regulation and the spirit of the constitution. Under this interpretation, the review of the competent agency would focus on the sufficiency of biobanks’ standard operating procedures (SOPs) and contracts with applicants in ensuring adequate protection of biological material derivatives and personal data.