Background: There has been a recent swell in activity by health research funding organizations and science journal editors to increase uptake of sex and gender considerations in study design, conduct and reporting in order to ensure that research results apply to everyone. However, examination of the implementation research literature reveals that attention to sex and gender has not yet infiltrated research methods in this field. Discussion: The rationale for routinely considering sex and gender in implementation research is multifold. Sex and gender are important in decision-making, communication, stakeholder engagement and preferences for the uptake of interventions. Gender roles, gender identity, gender relations, and institutionalized gender influence the way in which an implementation strategy works, for whom, under what circumstances and why. There is emerging evidence that programme theories may operate differently within and across sexes, genders and other intersectional characteristics under various circumstances. Furthermore, without proper study, implementation strategies may inadvertently exploit or ignore, rather than transform thinking about sex and gender-related factors. Techniques are described for measuring and analyzing sex and gender in implementation research using both quantitative and qualitative methods. Summary: The present paper describes the application of methods for integrating sex and gender in implementation research. Consistently asking critical questions about sex and gender will likely lead to the discovery of positive outcomes, as well as unintended consequences. The result has potential to strengthen both the practice and science of implementation, improve health outcomes and reduce gender inequities.