A charge pump circuit is provided. The charge pump circuit includes a pump unit, first through sixth switches, a fly capacitor and an output capacitor. In a first period, an input voltage and a first voltage charge at least one internal capacitor of the pump unit via a first terminal and a second terminal of the pump unit. In the second period, the internal capacitor of the pump unit provides charges to the fly capacitor via the second switch and generates a first output voltage. In the third period, the fly capacitor supplies the charges to the output capacitor via the fourth switch to generate a second output voltage.