\documentclass[monochrome]{fithesis3}
\usepackage{ifluatex}
\ifluatex
  \usepackage{polyglossia}
  \setmainlanguage{slovak}
\else
  \usepackage[slovak]{babel}
\fi
\thesissetup{
  faculty=sci,
  gender=f}
\begin{document}
  foo bar
\end{document}
