An apparatus for fabricating a 3D scaffold includes: a plotter generating a microfiber structure; an electrospinning unit installed to be adjacent to the plotter along a first direction and spinning nanofiber in an internal space or on a surface of the microfiber structure to form a nanofiber web; a collection table reciprocating a lower portion of the plotter and that of the electrospinning unit along the first direction to allow the microfiber structure to be stacked thereon by the plotter and allow the nanofiber web to be formed thereon by the electrospinning unit; and a first guide rail allowing the collection table to be mounted thereon and guiding the collection table mounted thereon to reciprocate along the first direction.