If you are using Jekyll (GitHub’s default), add mathjax: true to the YAML front matter of the markdown document that needs it.

Then add this to _config.yml:

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markdown: kramdown
kramdown:
  input: GFM                            # use Github Flavored Markdown !important
  syntax_highlighter_opts:
    span:
      line_numbers: false
    block:
      line_numbers: true
      start_line: 1

Then in _includes/mathjax_support.html — if it does not exist, put it in head.html, or whatever file plays the role of “head”, but prefer the one named after mathjax — add:

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<script type="text/x-mathjax-config">MathJax.Hub.Config({tex2jax: {inlineMath: [['$','$'], ['\\(','\\)']]}});</script>
<script type="text/javascript" async src="//cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-MML-AM_CHTML"></script>

That should fix it.