To obtain a superconducting junction element and its manufacturing method in which a superconducting junction having enhanced integration and planarity can be implemented easily.

The superconducting junction element comprises a recess 21A formed on a substrate 21 of LSAT in the pattern of lower electrode 22E or wiring, a first superconducting layer 22 filling the recesses 21A, a trench 25 made to form an inclination, i.e., a ramp 22R, for forming a junction at a part of the first superconducting layer 22, and a second superconducting layer 26 for filling the trench 25 to form a junction to the first superconducting layer 22.