Implementation research is a multidisciplinary field that addresses the complex phenomenon of how context influences our ability to deliver evidence-informed healthcare. There is increasing realisation of the importance of applying robust implementation research to scale-up life-saving interventions that meet health-related sustainable development goals. However, the lack of high-quality implementation research is impeding our ability to meet these targets, globally. Within implementation research, theory refers to the proposed hypothesis and/or explanation of how an intervention is expected to interact with the local context and actors to bring about change. Although there is increasing interest in applying theory to understand how and why implementation programmes work in real-world settings, global health actors still tend to favour impact evaluations conducted in controlled environments. This may, in part, be due to the relative novelty as well as methodological complexity of implementation research and the need to draw on divergent disciplines, including epidemiology, implementation science and social sciences. Because of this, implementation research is faced with a particular set of challenges about how to reconcile different ways of thinking and constructing knowledge about healthcare interventions. To help translate some of the ambiguity surrounding how divergent theoretical approaches and methods contribute to implementation research, we draw on our multidisciplinary expertise in the field, particularly in global health. We offer an overview of the different theoretical approaches and describe how they are applied to continuously select, monitor and evaluate implementation strategies throughout the different phases of implementation research. In doing so, we offer a relatively brief, user-focused guide to help global health actors implement and report on evaluation of evidence-based and scalable interventions, programmes and practices.