System and method for controlled atmosphere stunning of chickens in a batch mode is provided. The disclosed method includes the steps of: loading one or more batches of chickens in a stunning chamber and sealably enclosing the stunning chamber to isolate the atmosphere therein. Carbon dioxide is then introduced to the isolated atmosphere in a series of three, four or five phases to humanely stun the chickens. The carbon dioxide containing atmosphere is subsequently forcibly exhausted from the stunning chamber and the ranks of cages or modules containing the stunned chickens are advanced to the tipper or dumping station.