I am using MiKTeX 2.9 on Windows 7.
When I use the following to add a footnote to a section header
\section{Section Name}\footnote{Footnote text.}
\label{sec:SectionLabel}
I get the superscript for the footnote as a separate paragraph in the section. When I try
\section{Section Name\protect\footnote{Footnote text.}}
\label{sec:SectionLabel}
I get a compile error
! TeX capacity exceeded, sorry [input stack size=5000].
which I don't get otherwise since it is a fairly small document (33 pages).
Edit: The compilable latex code is as follows.
\documentclass[twocolumn]{article}
\usepackage{MnSymbol}
\usepackage{amsmath} % Required to use \text
\usepackage[normalem]{ulem} % Use ulem with normal (as opposed to underlined) emphasis option
\usepackage[T1]{fontenc} % Use 8-bit encoding that has 256 glyphs
\usepackage{datetime}
\usepackage[hmarginratio=1:1,top=32mm,columnsep=20pt]{geometry} % Document margins
\usepackage[hang, small,labelfont=bf,up,textfont=it,up]{caption} % Custom captions under/above floats in tables or figures
\usepackage{booktabs} % Horizontal rules in tables
\usepackage{float} % Required for tables and figures in the multi-column environment - they need to be placed in specific locations with the [H] (e.g. \begin{table}[H])
\usepackage{hyperref} % For hyperlinks in the PDF
\usepackage{mathtools}
\DeclarePairedDelimiter{\ceil}{\lceil}{\rceil}
\DeclarePairedDelimiter{\floor}{\lfloor}{\rfloor}
\usepackage{lettrine} % The lettrine is the first enlarged letter at the beginning of the text
\usepackage{paralist} % Used for the compactitem environment which makes bullet points with less space between them
\usepackage{abstract} % Allows abstract customization
\renewcommand{\abstractnamefont}{\normalfont\bfseries} % Set the "Abstract" text to bold
\renewcommand{\abstracttextfont}{\normalfont\small\itshape} % Set the abstract itself to small italic text
\usepackage{titlesec} % Allows customization of titles
\titleformat{\section}[block]{\large\scshape\centering}{\thesection.}{1em}{} % Change the look of the section titles
\titleformat{\subsection}[block]{\large}{\thesubsection.}{1em}{} % Change the look of the section titles
\usepackage{fancyhdr} % Headers and footers
\pagestyle{fancy} % All pages have headers and footers
\fancyhead{} % Blank out the default header
\fancyfoot{} % Blank out the default footer
\fancyhead[C]{ Title $\bullet$ \date{\today}} % Custom header text
\fancyfoot[RO,LE]{\thepage} % Custom footer text
\usepackage{graphicx}
\usepackage{rotating}
\usepackage{amsfonts} % For number set symbols
\usepackage{appendix}
\usepackage{color}
\usepackage{amsmath}
\usepackage{algorithm}
\usepackage[noend]{algpseudocode}
\makeatletter
\def\BState{\State\hskip-\ALG@thistlm}
\makeatother
%----------------------------------------------------------------------------------------
% TITLE SECTION
%----------------------------------------------------------------------------------------
\title{\vspace{-15mm}\fontsize{24pt} {10pt}\selectfont\textbf{Title}} % Article title
\author{
\large
\textsc{Name}\thanks{Thankee}\\[2mm]
\normalsize Address \\ Address, cont\\
\vspace{-5mm}
}
\date{}
%----------------------------------------------------------------------------------------
\begin{document}
\maketitle % Insert title
\thispagestyle{fancy} % All pages have headers and footers
\section{Section Name}\footnote{Footnote text.}
\label{sec:SectionLabel}
\end{document}
Further edited to add version number
\section[Section Name]{Section Name\footnote{Whatever}}