Bring the water up to a boil, then lower it to a rapid simmer. Add the eggs to the pot, and then begin timing. If you're just cooking one or two eggs, five minutes is perfect for a runny yolk, or cook as long as seven minutes for a more firmly set, but still spoonable, yolk.ently lower the eggs into the water one at a time. Cook the eggs for 5 to 7 minutes: For 1 to 2 eggs, cook 5 minutes for a very runny yolk or up to 7 minutes for a barely-set yolk. For 3 or 4 eggs, add a few extra seconds to your timing.