Modern engineering technology often involves the physical application of heat and mass transfer. These processes are associated with the creeping motion of a relatively homogeneous swarm of small particles, where the spheroidal geometry represents the shape of the embedded particles within such aggregates. Here, the steady Stokes flow of an incompressible, viscous fluid through an assemblage of particles, at low Reynolds numbers, is studied by employing a particle-in-cell model. The mathematical formulation adopts the Kuwabara-type assumption, according to which each spheroidal particle is stationary and it is surrounded by a confocal spheroid that creates a fluid envelope, in which the Newtonian fluid moves with a constant velocity of arbitrary orientation. The boundary value problem in the fluid envelope is solved by imposing non-slip conditions on the surface of the spheroid, which is also considered as non-penetrable, while zero vorticity is assumed on the fictitious spheroidal boundary along with a uniform approaching velocity. The three-dimensional flow fields are calculated analytically for the first time, in the spheroidal geometry, by virtue of the Papkovich–Neuber representation. Through this, the velocity and the total pressure fields are provided in terms of a vector and the scalar spheroidal harmonic potentials, which enables the thorough study of the relevant physical characteristics of the flow fields. The newly obtained analytical expressions generalize to any direction with the existing results holding for the asymmetrical case, which were obtained with the aid of a stream function. These can be employed for the calculation of quantities of physical or engineering interest. Numerical implementation reveals the flow behavior within the fluid envelope for different geometrical cell characteristics and for the arbitrarily-assumed velocity field, thus reflecting the different flow/porous media situations. Sample calculations show the excellent agreement of the obtained results with those available for special geometrical cases. All of these findings demonstrate the usefulness of the proposed method and the powerfulness of the obtained analytical expansions.