Background Health researchers are increasingly using social media in a professional capacity, and the applications of social media for health researchers are vast. However, there is currently no published evidence synthesis of the ways in which health researchers use social media professionally, and uncertainty remains as to how best to harness its potential. Objective This scoping review aimed to explore how social media is used by health researchers professionally, as reported in the literature. Methods The scoping review methodology guided by Arksey and O’Malley and Levac et al was used. Comprehensive searches based on the concepts of health research and social media were conducted in MEDLINE, EMBASE, CINAHL, PsycINFO, ERIC, and Web of Science databases, with no limitations applied. Articles were screened at the title and abstract level and at full text by two reviewers. One reviewer extracted data that were analyzed descriptively to map the available evidence. Results A total of 8359 articles were screened at the title and abstract level, of which 719 were also assessed at full text for eligibility. The 414 articles identified for inclusion were published in 278 different journals. Studies originated from 31 different countries, with the most prevalent being the United States (52.7% [218/414]). The health discipline of the first authors varied, with medicine (33.3% [138/414]) being the most common. A third of the articles covered health generally, with 61 health-specific topics. Papers used a range of social media platforms (mean 1.33 [SD 0.7]). A quarter of the articles screened reported on social media use for participant recruitment (25.1% [104/414]), followed by practical ways to use social media (15.5% [64/414]), and use of social media for content analysis research (13.3% [55/414]). Articles were categorized as celebratory (ie, opportunities for engagement, 72.2% [299/414]), contingent (ie, opportunities and possible limitations, 22.7% [94/414]) and concerned (ie, potentially harmful, 5.1% [21/414]). Conclusions Health researchers are increasingly publishing on their use of social media for a range of professional purposes. Although most of the sentiment around the use of social media in health research was celebratory, the uses of social media varied widely. Future research is needed to support health researchers to optimize their social media use.