We here present the first results of fully three-dimensional MHD simulations of radiative cooling pulsed (time-variable) jets for a set of parameters that are suitable for protostellar outflows. Considering different initial magnetic field topologies in approximate equipartition with the thermal gas, i.e., (1) a longitudinal and (2) a helical field, both of which permeate the jet and the ambient medium, and (3) a purely toroidal field permeating only the jet, we find that the overall morphology of the pulsed jet is not very much affected by the presence of the different magnetic field geometries in comparison with a nonmagnetic calculation. Instead, the magnetic fields tend to affect essentially the detailed structure and emission properties behind the shocks at the head and at the pulse-induced internal knots, particularly for the helical and toroidal geometries. In these cases, we find, for example, that the Hα emissivity behind the internal knots can be about 3-4 times larger than that of the purely hydrodynamical jet. We also find that some features, like the nose cones that often develop at the jet head in two-dimensional calculations involving toroidal magnetic fields, are smoothed out or absent in the three-dimensional calculations.