Melnikovs method is an analytical way to show the existence of classical chaos generated by a Smale horseshoe. It is a powerful technique, though its applicability is somewhat limited. In this paper, we present a solution of type IIB supergravity to which Melnikovs method is applicable. This is a brane-wave type deformation of the AdS$_5times$S$^5$ background. By employing two reduction ansatze, we study two types of coupled pendulum-oscillator systems. Then the Melnikov function is computed for each of the systems by following the standard way of Holmes and Marsden and the existence of chaos is shown analytically.