A control system for controlling electromagnetic pumps, such as electromagnetic driven membrane pumps, has at least one microprocessor and at least one sensor, the microprocessor controlling 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 has at least one positioning sensor which senses the moving part's position in the electromagnetic driven pump. By use of the positioning sensor's measurements, the pump can be controlled with great accuracy. A method for controlling electromagnetic pumps is also provided.