This study investigates the impact of vascular flow rate on the efficiency of sonoporation in viable mesenteric arteries ((391 ± 35) μm in intralumenal diameter), shedding light on the applications of ultrasound and microbubble-mediated (USMB) therapies. Isolated viable rat mesenteric arteries, which retained physiological functionality, exhibited reversible responses to vasoactive agents when mounted on a pressure myograph throughout the experiments. We then subjected these vessels to ultrasound (2.25 MHz) and microbubble treatment (Definity) under varied acoustic and flow conditions and assessed sonoporation through propidium iodide (PI) fluorescence microscopy. Results disclosed a strong correlation between microbubble flow rate, duty cycle, and sonoporation efficiency. Higher flow rates and duty cycles were associated with increased PI-positive cell counts, signifying more efficient cellular permeability. Post-treatment viability assays affirmed vessel integrity. These findings underscore the pivotal role of vascular flow rate in shaping therapeutic efficacy within individual vessels. The implications extend to refining USMB therapies in diverse disease scenarios, emphasizing the necessity for meticulous parameter selection to ensure both effectiveness and safety. Overall, the study furnishes valuable insights for enhancing the success and applicability of USMB-based therapeutic approaches in cardiovascular and oncological contexts.