Many gastric motility disorders, including gastroparesis, are caused by dysrhythmias occurring in the stomach musculature. Microwave ablation (MWA) offers potential as a minimally invasive endoscopic approach for targeted thermal destruction of the gastric musculature to disrupt irregular electrical rhythm within the stomach wall. An experimental study was conducted in a gel phantom to analyze the transient heating profile of a water-cooled 2.45 GHz MWA antenna enclosed within a PET balloon. Fiber-optic temperature sensors were used to collect temperature data at distances 1.5–7.5 mm from the balloon surface. Ablation profiles were also characterized in ex vivo porcine skeletal muscle. With 20 W applied power and cooling water temperature of 5 °C, temperature measured at 3.5 mm from the balloon surface exceeded the temperature at 1.5 mm from the balloon surface by 3 °C. In ex vivo tissue, for 40 W applied power, tissue within 2 mm of the balloon surface remained unablated. With adequate cooling and power, it may be feasible to thermally spare tissue within 2 mm of the MWA balloon applicator.