We investigate the ground state properties of ultracold atoms trapped in a two-leg ladder potential in the presence of an artificial magnetic field in a staggered configuration. We focus on the strongly interacting regime and use the Landau theory of phase transitions and a mean field Gutzwiller variational method to identify the stable superfluid phases and their boundaries with the Mott-insulator regime as a function of magnetic flux. In addition, we calculate the local and chiral currents of these superfluid phases, which show a staggered vortex anti-vortex configuration. The analytical results are confirmed by numerical simulations using a cluster mean-field theory approach.