Alkaline-earth(-like) ultracold atoms, trapped in optical lattices and in the presence of an external gauge field, can stabilise Mott insulating phases characterised by density and magnetic order. We show that this property can be used to realise a topological fractional pump. Our analysis is based on a many-body adiabatic expansion and on time-dependent matrix-product-states numerical simulations. We characterise the pumping protocol by including both finite-size and non-adiabatic corrections. For a specific form of atom-atom interaction, we present an exactly-solvable model of a fractional pump. Finally, the numerical simulations allow us to thoroughly study a realistic setup amenable of an experimental realisation.