How to tell when the halibut is done. Pull the rack just far enough out of the oven to be able to test with a fork. Using the back of a fork, press down on fillet. If the fillet starts to flake, it's cooked. Depending on your oven, the fish will take about 3-4 minutes per 1/2-inch thickness. It's best just to watch it close and check on it every 4 minutes.