A programmable switching circuit with charge pumps for a bio-stimulator is disclosed. A programmable controlling circuit generates a set of binary bits according to a controlling program and then uses a universal asynchronous receiver/transmitter for outputting to the pulse signal generating circuit so as to generate two pulse signals with the predetermined waveforms and different phases. Then, according to these two pulse signals with different phases, two charge pumps included in a charge pump regulating circuit output currents with specific voltage intensity through two output routes. The amplitude of the current is determined by the capacitor on each output route. Additionally, the programmable controlling circuit determines which route to be outputted so as to control and switch the polarities and current amplitude of a bio-stimulator.