1. Put kombu and 2 cups water in a small pan. Bring to a simmer over medium-low heat, about 20 minutes. Just before water begins to bubble, discard kombu.
2. Increase heat to high and bring to a boil. Add bonito flakes, pressing with a spoon to submerge, and immediately shut off heat. Let flakes settle to bottom of pot, about 15 minutes.
3. Strain through a cheesecloth-lined strainer into a bowl. Wring out all liquid from cheesecloth into bowl.
Make ahead: Up to 2 hours at room temperature.
Note: Nutritional analysis is per cup.