A gas cylinder charging system includes (1) at least two gas inlet ports and (2) at least two gas outlet ports, (3) a gas compressor having an input port and an output port, where the input port selectively receives gas from a gas inlet port and selectively transfers the gas to a gas outlet port, and (4) a controller, receiving status signals and transmitting control signals, and connected to and controlling the gas compressor. A method aspect of filling a gas cylinder using the described cylinder charging system further including an input/output selector valve for selecting one of the gasses to transfer to the gas cylinder, includes the following steps. A gas cylinder is connected to one of the cylinder connectors. A user manipulates the selector valve selecting the gas to be transferred to the gas cylinder and activates the cylinder charging system filling the gas cylinder with the selected gas.