Regardless of where you choose to have your surgery, the cost of gastric bypass surgery will be higher if you have complications. For this reason, you should plan for the cost of gastric bypass surgery ahead of time so you don’t get stuck with a big bill due to complications. Better yet, have insurance so the average cost of gastric bypass surgery is at least partially covered. With insurance, the cost of gastric bypass surgery can be nothing at all or can be a percentage of the total charges.  The cost of gastric bypass surgery is nothing if you have Medicare but there are rigorous guidelines you must have before qualifying.