In this study, a boundary element method (BEM) is applied to investigate acoustic radiation from a sphere vibrating in pulsating mode on the free surface of finite or infinite depth water. Effect of the free surface is introduced by employing a half-space Green’s function. A modified version of the Helmholtz integral equation (HIE) is used to calculate acoustic radiation from the sphere vibrating in pulsating mode on the free surface. Free-terms of the HIE are calculated using two different forms of integrals and “dummy” boundary elements. Moreover, to simulate finite depth fluid medium, a chain image-source method is used to derive a waveguide Green’s function. To demonstrate applicability of the method presented, calculated acoustic pressures are compared with those by finite element method (FEM) and analytical calculations. Additionally, the effects of submergence depth and vibration frequency on acoustic radiation are investigated for infinitely deep water together with those of water depth and field point distance on acoustic radiation for finite water depth medium. The calculations show that there is a good agreement between BEM, FEM and analytical solutions. Also, it is observed that field point distance significantly affects the convergence behavior of waveguide Green’s function. Furthermore, it is noted that submergence depth, domain depth and vibration frequency have pronounce influence on radiated pressure amplitude and pressure field pattern.