In a small bowl, stir together the soy sauce, honey, garlic, and 2 teaspoons of the sesame oil.
Heat a 10-inch cast-iron skillet over medium-high heat.
Meanwhile, in a medium bowl, toss together the shishito peppers and the remaining 1 tablespoon sesame oil to thoroughly coat.
Add the shishito peppers to the skillet and cook until blistered, making sure to stir peppers about every minute to allow for even blistering, about 10 minutes. Return the peppers to the medium bowl.
Add the garlic-soy sauce mixture to the peppers and toss to coat. Transfer to a serving bowl and garnish with the sesame seeds and red pepper flakes.