High-quality Schottky junctions have been fabricated on n-type 4H SiC epitaxial layers grown by chemical-vapor deposition on C- and Si-face substrates in order to understand the effect of growth direction on the growth mechanism and formation of defects. Atomic force microscopy analysis showed dramatic differences between the surfaces of SiC epilayers grown on C and Si faces. There was a significant step bunching in the SiC grown on Si-face substrates. Current-voltage, capacitance-voltage, and deep-level transient spectroscopy (DLTS) measurements were carried out on the Schottky junctions to analyze the junction characteristics. The Schottky junctions on C-face SiC showed larger barrier heights than those on Si-face SiC, showing that each face has a different surface energy. The barrier heights of Ni Schottky junctions were found to be 1.97 and 1.54 eV for C-face and Si-face materials, respectively. However, the deep-level spectra obtained by DLTS were similar, regardless of the increased surface roughness of the Si-face 4H SiC.