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Brain-Computer Interfaces (BCIs) comprise a rapidly evolving field of technology with the potential of far-reaching impact in domains ranging from medical over industrial to artistic, gaming, and military. Today, these emerging BCI applications are typically still at early technology readiness levels, but because BCIs create novel, technical communication channels for the human brain, they have raised privacy and security concerns. To mitigate such risks, a large body of countermeasures has been proposed in the literature, but a general framework is lacking which would describe how privacy and security of BCI applications can be protected by design, i.e., already as an integral part of the early BCI design process, in a systematic manner, and allowing suitable depth of analysis for different contexts such as commercial BCI product development vs. academic research and lab prototypes. Here we propose the adoption of recent systems-engineering methodologies for privacy threat modeling, risk assessment, and privacy engineering to the BCI field. These methodologies address privacy and security concerns in a more systematic and holistic way than previous approaches, and provide reusable patterns on how to move from principles to actions. We apply these methodologies to BCI and data flows and derive a generic, extensible, and actionable framework for brain-privacy-preserving cybersecurity in BCI applications. This framework is designed for flexible application to the wide range of current and future BCI applications. We also propose a range of novel privacy-by-design features for BCIs, with an emphasis on features promoting BCI transparency as a prerequisite for informational self-determination of BCI users, as well as design features for ensuring BCI user autonomy. We anticipate that our framework will contribute to the development of privacy-respecting, trustworthy BCI technologies.