Cook the eggs for up to 12 minutes. Set your microwave on medium power and begin microwaving the eggs. The eggs may take anywhere from six to 12 minutes to become hard boiled, depending on your microwave. The eggs may be ready sooner if your microwave is high-powered or if you prefer your eggs softer. If you poured boiling water over your eggs, then you can just cook them for three to six minutes on high.