A method is disclosed for controlling a simulated moving bed system of a type including at least four series-arranged beds each packed with a solid adsorbent, with the downstream end of each bed and the upstream end of the next succeeding bed being connected by conduits to form an endless loop, and in which a fluid is caused to circulate through the beds in one direction, a feed stock and a desorbent are introduced into the system while a raffinate and a sorbate are withdrawn from the system, and the positions of introduction and withdrawal of the four kinds of fluid are periodically shifted in the direction of the circulating fluid flow. In accordance with the invention, two or more circulating pumps, provided with variable speed controllers and pressure detectors for detecting the suction pressure of each of the circulating pumps, are disposed between two beds. The flow rates of three of the four fluids introduced into or withdrawn from the system are adjusted to predetermined values, and the flow rate of the other fluid is controlled in such a manner that the suction pressure of one of the circulating pumps or the average of the suction pressures of two or more of the circulating pumps is held constant, and a rotational speed of each of the circulating pumps is controlled independently so as to control the flow rate of the circulating fluid and to maintain the suction pressure of each circulating pump at a low level.