The surface tension of quark matter plays a crucial role for the possibility of quark matter nucleation during the formation of compact stellar objects and also for the existence of a mixed phase within hybrid stars. However, despite its importance, this quantity does not have a well established numerical value. Some early estimates have predicted that, at zero temperature, the value falls within the wide range γ0 ≈ 10 − 300 MeV/fm 2 but, very recently, different model applications have reduced these numerical values to fall within the range γ0 ≈ 5 − 30 MeV/fm 2 which would favor the phase conversion process as well as the appearance of a mixed phase in hybrid stars. In magnetars one should also account for the presence of very high magnetic fields which may reach up to about eB ≈ 3 − 30 m 2 π (B ≈ 10 19 − 10 20 G) at the core of the star so that it may also be important to analyze how the presence of a magnetic field affects the surface tension. With this aim we consider magnetized two flavor quark matter, described by the Nambu-Jona-Lasinio model. We show that although the surface tension oscillates around its B = 0 value, when 0 < eB < ∼ 10 m 2 π , it only reaches values which are still relatively small. For eB ≈ 5 m 2 π the B = 0 surface tension value drops by about 30% while for eB > ∼ 10 m 2 π it quickly raises with the field intensity so that the phase conversion and the presence of a mixed phase should be suppressed if extremely high fields are present. We also investigate how thermal effects influence the surface tension for magnetized quark matter.