Abstarct: In this research Fluid-Structure Interaction (FSI) during transient flow in a viscoelastic (VE) pipe has been studied in frequency domain. The main aim was to investigate water hammer problem using Transfer Matrix Method (TMM) in a typical reservoir-viscoelastic pipe-valve system. One of the generally expected advantage of frequency domain analysis is that the integral form of equations in time domain would be transformed to algebraic form. Here it was more beneficial to utilize frequency domain methods since convolution integral which appears in viscoelastic models in time domain will also be eliminated. TMM has been adopted to the transient flow in a VE pipe to derive field matrix where a non-oscillating valve is considered as boundary condition. The generalized Kelvin-Voigt model was used to simulate the viscoelastic behavior of the pipe wall. The proposed model has been exploited to solve two well-known case studies of FSI in frequency domain. Results of both cases shows good agreement with the analytical and experimental data. To investigate the simultaneous effects of viscoelasticity and FSI in frequency domain a sample problem has been solved. Results of different cases of interactional and non-interactional analysis and for viscoelastic and elastic pipe material have been illustrated for comparison. Also a comparison between three, five and higher number of Kelvin-Voigt elements has been performed to illustrate the possible improvement in the simulation.