IntroductionMore than one-third of the world population uses at least one form of social media. Since their advent in 2005, health-oriented research based on social media data has largely increased as discussions about health issues are broadly shared online and generate a large amount of health-related data. The objective of this scoping review is to provide an evidence map of the various uses of social media for health research purposes, their fields of applications and their analysis methods.Methods and analysisThis scoping review will follow the Arksey and O’Malley methodological framework (2005) as well as the Joanna Briggs Institute Reviewer’s manual. Relevant publications will be first searched on the PudMed/MEDLINE database and then on Web of Science. We will focus on literature published between January 2005 and April 2020. All articles related to the use of social media or networks for health-oriented research purposes will be included. A first search will be conducted with some keywords in order to identify relevant articles. After identifying the research strategy, a two-part study selection process will be systematically applied by two reviewers. The first part consists of screening titles and abstracts found, thanks to the search strategy, to define the eligibility of each article. In the second part, the full texts will be screened and only relevant articles will be kept. Data will finally be extracted, collated and charted to summarise all the relevant methods, outcomes and key findings in the articles.Ethics and disseminationThis scoping review will provide an extensive overview of the use of social media for health research purposes. Opportunities as well as future ethical, methodological and technical challenges will also be discussed based on our findings to define a new research agenda. Results will be disseminated through a peer-reviewed publication.