documentclass{beamer}

usepackage{amsthm}
newtheorem{theorem}{Theorem}

usepackage{etoolbox}

begin{document}

begingroup
apptocmd{thetheorem}{protectfootnote{A footnote.}}{}{}

begin{theorem}
Some text.
end{theorem}

endgroup

begin{theorem}
Some text.
end{theorem}

end{document}