A method and apparatus for the humane euthanasia of small animals involves the use of a programmable controller and animal holding chamber. The apparatus includes a Mass Flow Controller (“MFC”) having a closed-loop interface with a Programmable Logic Controller (“PLC”) to provide a predetermined flow rate of gas under specified pressures for specified time periods. The PLC is preprogrammed to provide various cycles that are designed to provide the proper flow rate for various animal species. The program may allow for a two-stage flow rate cycle so that in the first stage the animal is anesthetized and in the second stage the animals are euthanatized.