A three-dimensional (3D) numerical simulation was performed using a combined stroke swimmer (deformable sphere) in an incompressible fluid of an infinite domain. The time-dependent deformation of the swimmer surface was assumed independent of the circumferential cross section in the flow direction of the swimmer. The 3D numerical simulation is an extension of our previous study that considered an axisymmetric numerical simulation. In particular, different fluid viscosities were considered for the same stroke of the swimmer. The effect of the swimmer inertia was studied by gradually decreasing the fluid viscosity. When the fluid viscosity decreased, the mean velocity of the swimmer changed its direction between Re = 0.00189 and Re = 0.0103. There is a transition between Re = 0.0103 and Re = 9.90 from the axisymmetric to three-dimensional flow that exhibits planar symmetry.