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In the present paper, we summarize the results of the research devoted to the problem of stability of the fluid flow moving in a channel with flexible walls and interacting with the walls. The walls of the vessel are subject to traveling waves. Experimental data show that the energy of the flowing fluid can be transferred and consumed by the structure (the walls), inducing “traveling wave flutter.” The problem of stability of fluid-structure interaction splits into two parts: (a) stability of fluid flow in the channel with harmonically moving walls and (b) stability of solid structure participating in the energy exchange with the flow. Stability of fluid flow, the main focus of the research, is obtained by solving the initial boundary value problem for the stream function. The main findings of the paper are the following: (i) rigorous formulation of the initial boundary problem for the stream function, ψ x , y , t , induced by the fluid-structure interaction model, which takes into account the axisymmetric pattern of the flow and “no-slip” condition near the channel walls; (ii) application of a double integral transformation (the Fourier transformation and Laplace transformation) to both the equation and boundary and initial conditions, which reduces the original partial differential equation to a parameter-dependent ordinary differential equation; (iii) derivation of the explicit formula for the Fourier transform of the stream function, ψ ˜ k , y , t ; (iv) evaluation of the inverse Fourier transform of ψ ˜ k , y , t and proving that reconstruction of ψ x , y , t can be obtained through a limiting process in the complex k -plane, which allows us to use the Residue theorem and represent the solution in the form of an infinite series of residues. The result of this research is an analytical solution describing blood flowing through a channel with flexible walls that are being perturbed in the form of a traveling wave.