Chapter title in header too long

Another alternative might be:

\chapter[medium-length title for TOC, if wanted]{full title name}
\chaptermark{short title for running headers}

You could provide a shorter chapter title via the optional argument to \chapter:

\chapter[<short title>]{<long title>}

Note that this will also influence the entry in the table of contents.

The solution that seems to work in every situation (even with math) is:

\chapter[\texorpdfstring{TOC title \( inline math A \)
    }{TOC in pdf bookmarks}
]{\chaptermark{header} Chapter title \( inline math A \)}
\chaptermark{header}
\label{CH:Chap}

In this solution the pdf bookmarks are defined by \texorpdfstring{#1}{#2}, where #1 is the title inside the pdf document while #2 is the pdf bookmark.

The [shorter] heading is defined by \chaptermark{header}. The repeated command is not a typo, but it is needed in order to have the right behaviour in every situation (do not ask why since I do not have any idea, just by tentative; if you know the reason, please comment. EDIT (2016-03-22): Some explanations can be found HERE)

Important: the solution also works with \section, just change \chaptermark with \sectionmark.

Disclaimer: I wrote the blog post.