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A method of noncollocated controller design for non-uniform flexible structures, governed by the wave equation, is proposed. An exact, infinite dimensional, transfer function, relating the actuation and measurement points, with general boundary conditions, is derived for the multi-link case. Three modeling methods are presented and discussed. A key element of the model is the existence of time delays, due to the wave motion, which play a major role in the controller design. The design consists of two stages. First an inner rate loop is closed in order to improve the system dynamic behavior. It leads to a finite dimensional plus delay inner closed loop, which is the equivalent plant for the outer loop. In the second stage an outer noncollocated position loop is closed. It has the structure of an observer–predictor control scheme to compensate for the response delay. The resulting overall transfer function is second order, with arbitrarily assigned dynamics, plus delay.