We report the coexistence of the Kondo effect and spin glass behavior in Fe-doped NbS$_2$ single crystals. The Fe$_x$NbS$_2$ shows the resistance minimum and negative magnetoresistance due to the Kondo effect, and exhibits no superconducting behavior at low temperatures. The resistance curve follows a numerical renormalization-group theory using the Kondo temperature $T_K =12.3$~K for $x=0.01$ as evidence of Kondo effect. Scanning tunneling microscope/spectroscopy (STM/STS) revealed the presence of Fe atoms near sulfur atoms and asymmetric spectra. The magnetic susceptibility exhibits a feature of spin glass. The static critical exponents determined by the universal scaling of the nonlinear part of the susceptibility suggest a three-dimensional Heisenberg spin glass. The doped-Fe atoms in the intra- and inter-layers revealed by the X-ray result can realize the coexistence of the Kondo effect and spin glass.