Method for delivery remains a central component of stem cell-based cardiovascular research. Comparative studies have demonstrated the advantages of administering cell therapy directly into the myocardium, as distinct from infusing cells into the systemic or coronary vasculature. Intramyocardial delivery can be achieved either transepicardially or transendocardially. The latter involves percutaneous, femoral arterial access and the retrograde passage of specially designed injection catheters into the left ventricle, making it less invasive and more relevant to wider clinical practice. Imaging-based navigation plays an important role in guiding catheter manipulation and directing endomyocardial injections. The most established strategy for three-dimensional, intracardiac navigation is currently endoventricular, electromechanical mapping, which offers superior spatial orientation compared to simple x-ray fluoroscopy. Its provision of point-by-point, electrophysiologic and motion data also allows characterization of regional myocardial viability, perfusion, and function, especially in the setting of ischemic heart disease. Integrating the mapping catheter with an injection port enables this diagnostic information to facilitate the targeting of intramyocardial stem cell delivery. This review discusses the diagnostic accuracy and expanding therapeutic application of electromechanical navigation in cell-based research and describes exciting developments which will improve the technology’s sensing capabilities, image registration, and delivery precision in the near future.