In the present paper, the problems of longitudinal and flexural vibrations of an inhomogeneous rod are considered. The Young’s modulus and density are variable in longitudinal coordinate. Vibrations are caused by a load applied at the right end. The proposed method allows us to consider a wider class of inhomogeneity laws in comparison with other numerical solutions. Sensitivity analysis is carried out. A new inverse problem related to the simultaneous identification of the variation laws of Young’s modulus and density from amplitude–frequency data, which are measured in given frequency ranges, is considered. Its solution is based on an iterative process: at each step, a system of two Fredholm integral equations of the first kind with smooth kernels is solved numerically. The analysis of the kernels is carried out for different frequency values. To find the initial approximation, several approaches are proposed: a genetic algorithm, minimization of the residual functional on a compact set, and additional information about the values of the sought-for functions at the ends of the rod. The Tikhonov regularization and the LSQR method are proposed. Examples of reconstruction of monotonic and non-monotonic functions are presented.