We numerically show that a topologically nontrivial 3D Skyrmion can be energetically stable in a trapped two-component atomic Bose-Einstein condensate, for the parameters of Rb-87 condensate experiments. The separate conservation of the two atomic species can stabilize the Skyrmion against shrinking to zero size, while drift of the Skyrmion due to the trap-induced density gradient can be prevented by rotation or by a laser potential.