The measurement of flow-mediated dilation using high-resolution ultrasound has been utilized extensively in interventional trials evaluating the salutary effect of drugs and lifestyle modifications (i.e. diet or exercise training) on endothelial function; however, until recently researchers have not used flow-mediated dilation to examine the role of a single bout of exercise on vascular function. Utilizing the acute exercise model can be advantageous as it allows for an efficient manipulation of exercise variables (i.e. mode, intensity, duration, etc.) and permits greater experimental control of confounding variables. Given that the application of flow-mediated dilation in the acute exercise paradigm is expanding, the purpose of this review is to discuss methodological and physiological factors pertinent to flow-mediated dilation in the context of acute exercise. Although the scientific rationale for evaluating endothelial function in response to acute exercise is sound, few concerns warrant attention when interpreting flow-mediated dilation data following acute exercise. The following questions will be addressed in the present review: Does the measurement of flow-mediated dilation influence subsequent serial measures of flow-mediated dilation? Do we need to account for diurnal variation? Is there an optimal time to measure post-exercise flow-mediated dilation? Is the post-exercise flow-mediated dilation reproducible? How is flow-mediated dilation interpreted considering the hemodynamic and sympathetic changes associated with acute exercise? Can the measurement of endothelial-independent dilation affect the exercise? Evidence exists to support the methodological appropriateness for employing flow-mediated dilation in the acute exercise model; however, further research is warranted to clarify its interpretation following acute exercise.