A mathematical model for the problem of wave diffraction by a floating fixed truncated vertical cylinder is formulated based on Boussinesq equations (BEs). Using Bessel functions in the velocity potentials, the mathematical problem is solved for second-order wave amplitudes by applying a perturbation technique and matching conditions. On the other hand, computational fluid dynamics (CFD) simulation results of normalized free surface elevations and wave heights are compared against experimental fluid data (EFD) and numerical data available in the literature. In order to check the fidelity and accuracy of the Boussinesq model (BM), the results of the second-order super-harmonic wave amplitude around the vertical cylinder are compared with CFD results. The comparison shows a good level of agreement between Boussinesq, CFD, EFD, and numerical data. In addition, wave forces and moments acting on the cylinder and the pressure distribution around the vertical cylinder are analyzed from CFD simulations. Based on analytical solutions, the effects of radius, wave number, water depth, and depth parameters at specific elevations on the second-order sub-harmonic wave amplitudes are analyzed.