Motivated by recent experiments in Gd3Ru4Al12, we demonstrate the emergence of atomic scale Skyrmions in interacting spins on a breathing kagome lattice with competing nearest neighbor ferromagnetic and next nearest neighbor antiferromagnetic exchange interactions. In the presence of an applied longitudinal magnetic field, the ground state magnetic order evolves from a helical phase at low fields to a Skyrmion phase at intermediate fields before finally entering a polarized phase at high fields. The size of each Skyrmion spans only two unit cells of the lattice, in contrast to tens to hundreds of unit cells in most chiral magnets. Furthermore, the Skyrmions are driven not by chiral interactions but by the interplay between competing exchange interactions and geometric frustration, just as in Gd3Ru4Al12 . When itinerant electrons are coupled to the localized moments, they exhibit the usual Skyrmion-driven topological Hall effect (THE) arising from the real space Berry curvature of the the Skyrmion texture. The small size of the Skyrmions in this system yield a strong local Berry curvature that results in an enhanced THE, which is investigated using a strong coupling approximation between the spins of the itinerant electrons and the localized moments. Our results will be crucial in understanding the experiments in Gd3Ru4Al12 and other members of the same family of metallic frustrated magnets.