Cook the egg. Place it in the microwave and cook it on the highest power setting for 35 seconds. When it's done cooking, remove the paper towel and inspect the egg. If the white is still liquid, put it back in the microwave and cook for an additional 10 or 15 seconds. If you want the yolk to stay runny, cook the egg at 50 percent power for about 60 seconds. 2  Keep cooking until the white is set but the yolk is still runny. 3  For a hard-cooked egg (similar to a hard-boiled egg) cook on the highest power setting for 60 seconds. 4  7 Edit step.