The best way to thaw Cool Whip is to leave it in the fridge for about 4-5 hours. But if you haven't planned ahead, you can still thaw it out rather quickly. 1). Remove the lid from the container and microwave it, on the default setting, in 30-second increments. You'll want to stir in between each time. This should take about 2 minutes. 2). Place the Cool Whip Container (sealed) in a bowl or sink full of cool water. It should be thawed in about 45 minutes. Do not leave the container on the counter to thaw as it contains dairy and bacteria could start to develop.