Provided is a gas fill fixture for use in lyophilization, a related system and method. The gas fill fixture includes a chassis, fill indicator and a lid, such that the chassis and lid together form a cavity for receiving a flexible lyophilization container. The system includes a lyophilization container, a lyophilizer and a gas fill fixture incorporating a chassis, a fill indicator and a lid. The method includes process steps for using the system to lyophilize a fluid.