Online communication with participants, including online recruitment, electronic informed consent, and data communication, is one of the fields to which information and communication technology (ICT) has been applied in medical research. Online communication provides various benefits, especially for genome research and rare disease research. However, ethical challenges that are derived from or exacerbated by online communication need to be addressed. Here, we present an overview of such ethical issues and provide practical guidance for the ethical implementation of ICT. We specify the ethical issues in the context of using online communication for medical research by an analysis based on the eight ethical principles for clinical research. Informed by this ethical context, we then develop a novel framework for the governance of medical research involving ICT, which consists of eight categories: five research processes (ie, design of research, recruitment, informed consent, data communication, and dissemination and return of results) and three overarching perspectives related to multiple processes of research (ie, access to research and online dialog, community involvement, and independent review). Finally, we present a practical guidance chart for researchers, patient partners, independent reviewers, and funding agencies. We believe that our study will contribute to the ethical implementation of online communication in medical research.