Noncommunicable diseases (NCDs) are the leading global causes of morbidity and mortality. It is important to develop and deliver effective NCD prevention programs, but these have been difficult to evaluate. Technical approaches differ, with academic researchers, practitioners and policy makers each bringing different perspectives and priorities to the task of NCD program evaluation. Epidemiologically defined hierarchies of research evidence give preference to evaluation methods that are often unsuitable for assessing complex NCD prevention interventions. This may lead to interventions that provide the 'right answer to the wrong question', or to evaluation data that are insufficient to inform NCD prevention efforts. This paper recommends a set of standardised stages in the planning, development and evaluation of NCD prevention programs, including the use of logic models, the expanded use of process evaluation to better understand and record the context for implementation, and the use of appropriate research designs for assessing the impact of both subcomponents and the whole program. NCD prevention agencies and academic stakeholders need to recognise the limitations of established evaluation designs and support greater flexibility in the application of evaluation methods that are fit for purpose in describing the stages in NCD programs. This involves assessing policy development and implementation, measuring intermediate indicators, using mixed methods of evaluation, and employing population surveillance systems to assess long-term outcomes.