I assume "doesn't work" means in this case "Generates the following error:"
! Use of \@xfootnotemark doesn't match its definition.
\@ifnextchar ... \reserved@d =#1\def \reserved@a {
#2}\def \reserved@b {#3}\f...
l.8 \maketitle
Right?
\thanks expands its argument (at least which the standard classes) and so you need to \protect the \input:
\documentclass{article}
\def\myTitle{My title}
\title{\myTitle\thanks{\protect\input{../acknowledgement}}}
\begin{document}
\maketitle
text
\end{document}
An alternative would be the catchfile package to store the content of the input file in a macro first using \CatchFileDef{\mymacro}{<file>}{}.