Graphical abstractDisplay Omitted Through Nb superconducting junction with Al-oxide current flow without voltage drop.Josephson current Ic dependence on Hx, Hy and Hz magnetic field was obtained.Ic dependence on Hx, Hy before applying Hz was Fraunhofer pattern.Ic dependence on Hx, Hy after applying Hz was not Fraunhofer pattern.Numerical simulation explained the measured dependence. Anomalous modulation characteristics of Josephson current Ic through niobium tunnel junctions at liquid helium temperature were first measured after applying the external magnetic field in perpendicular direction. Josephson current Ic was modulated by applying the external magnetic fields (Hx, Hy) parallel and Hz vertical to the junction plane. Modulation characteristics of the Ic value upon Hz had hysteresis. Before applying the vertical field, modulation characteristics Ic-(Hx, Hy) were the product of the two Fraunhofer diffraction patterns in Hx and Hy directions which were parallel to the junction edges of the square shape junction, respectively. Under the perpendicular magnetic field as much as 4000A/m, the maximum Ic value did not appear at (Hx, Hy)=(0, 0) point. After removing this vertical field, the Ic-(Hx, Hy) modulation pattern changed from the product of the two Fraunhofer diffraction patterns to the deformed Ic-(Hx, Hy) characteristics, whose anomalous shape was explained by assuming the extremely low current density at four edges of the square shape except the four corner regions. Some magnetic flux would be trapped perpendicularly inside the junction electrodes within the junction area. After the junction was heated to the room temperature and was again cooled to the liquid He temperature, these modulation characteristics again became the normal modulation pattern, in which the trapped flux would be released by this thermal cycle.