Alkaline-earth(-like) atoms, trapped in optical lattices and in the presence of an external gauge field, can form insulating states at given fractional fillings. We will show that, by exploiting these properties, it is possible to realize a topological fractional pump. Our analysis is based on a many-body adiabatic expansion, on simulations with time-dependent matrix product states, and, for a specific form of atom-atom interaction, on an exactly solvable model of fractional pump. The numerical simulations allow us to consider a realistic setup amenable of an experimental realization. As a further consequence, the measure of the center-of-mass shift of the atomic cloud would constitute the first measurement of a many-body Chern number in a cold-atom experiment.