A control system and method for controlling electromagnetic drive pumps as, for example, electromagnetic driven membrane pumps are provided in which the control system is formed by at least one microprocessor and at least one sensor, whose microprocessor controls the power supply to at least one electromagnet whose changes in emitted magnetic field causes at least one moving part, directly or indirectly, to perform an oscillating pumping movement. The control system includes at least one positioning sensor which senses the moving part's position in the electromagnetic driven pump. By using the positioning sensor's measurements, the pump can be controlled with great accuracy.