Background: Reflecting global norms, South Africa is associated with high levels of cross-border and internal population mobility, yet migration-aware health system responses are lacking. Existing literature highlights four methodological challenges limiting the development of evidence-informed responses to migration and health: (1) lack of engagement with the process of migration; (2) exclusion of internal migrants; (3) insufficient attention to the ways in which gender and other identity markers shape health systems access; and, (4) lack of methodologies that are able to capture ‘real-time’ data about health needs, healthcare seeking experiences, and interactions with healthcare systems over both time and place. In this paper, we reflect on a four-month pilot project which explored the use of WhatsApp Messenger - a popular mobile phone application used widely in sub-Saharan Africa – as a research tool to address these challenges. Results: A four-month pilot was undertaken with 11 participants between October 2019 and January 2020. Using Survey Node, an online platform that allows for the automatic administration of surveys through WhatsApp, monthly surveys were administered. The GPS coordinates of participants were also obtained. Recruited through civil society partners in Gauteng, participants were over the age of 18, comfortable engaging in English, and owned WhatsApp compatible cell phones. Enrolment involved an administered survey and training participants in the study protocol. Participants received reimbursement for their travel costs and cell phone data monthly. Out of a possible 88 survey and location responses, 61 were received. Findings emphasise the ethical and methodological challenges of using WhatsApp as a tool for data collection with migrant and mobile populations.Conclusions: The pilot demonstrates the potential of WhatsApp for addressing our concerns with the current state of research exploring migration and health. It suggests, through the ability to focus on the process of migration, including internal migration, and the opportunities it provides to elucidate the ways in which this process intersects with access to healthcare and gender, that WhatsApp has real potential as a research tool. The pilot informed finalisation of the main study, including ensuring that our approach and research met the ethical standards congruent with the method.