Synchrotron radiation is commonly observed in connection with shocks of different velocities, ranging from relativistic shocks associated with active galactic nuclei, gamma-ray bursts or microquasars to weakly- or non-relativistic flows as those observed in supernova remnants. Recent observations of synchrotron emission in protostellar jets are important not only because they extend the range over which the acceleration process works, but also because they allow to determine the jet and/or interstellar magnetic field structure, thus giving insights on the jet ejection and collimation mechanisms. In this paper, we compute for the first time polarized (synchrotron) and non polarized (thermal X-ray) synthetic emission maps from axisymmetrical simulations of magnetized protostellar jets. We consider models with different jet velocities and variability, as well as toroidal or helical magnetic field. Our simulations show that variable, low-density jets with velocities $sim$ 1000 km s$^{-1}$ and $sim$ 10 times lighter than the environment can produce internal knots with significant synchrotron emission, and thermal X-rays in the shocked region of the leading bow shock moving in a dense medium. While models with a purely toroidal magnetic field show a very large degree of polarization, models with helical magnetic field show lower values and a decrease of the degree of polarization, in agreement with observations of protostellar jets.