I found this to be the simplest way to integrate mathjax into Jekyll. This assumes you are using Kramdown as your markdown renderer, and your _config.yml contains the line markdown: kramdown

Here is the process:

  1. Create an _includes directory in your root Jekyll directory

  2. Create a file called mathjax.html inside it, and put the following inside the file 

     <script type="text/x-mathjax-config">
   MathJax.Hub.Config({
     extensions: [
       "MathMenu.js",
       "MathZoom.js",
       "AssistiveMML.js",
       "a11y/accessibility-menu.js"
     ],
     jax: ["input/TeX", "output/CommonHTML"],
     TeX: {
       extensions: [
         "AMSmath.js",
         "AMSsymbols.js",
         "noErrors.js",
         "noUndefined.js",
       ]
     }
   });
 </script>
 <script type="text/javascript" 
 src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js">
 </script>
  3. That’s it! When you’re creating a new page, just put this template tag at the top of your page 

     {% include mathjax.html %}
  4. You can now use the kramdown $$ syntax 

     $$
 \begin{align*}
   & \phi(x,y) = \phi \left(\sum_{i=1}^n x_ie_i, \sum_{j=1}^n y_je_j \right)
   = \sum_{i=1}^n \sum_{j=1}^n x_i y_j \phi(e_i, e_j) = \\
   & (x_1, \ldots, x_n) \left( \begin{array}{ccc}
       \phi(e_1, e_1) & \cdots & \phi(e_1, e_n) \\
       \vdots & \ddots & \vdots \\
       \phi(e_n, e_1) & \cdots & \phi(e_n, e_n)
     \end{array} \right)
   \left( \begin{array}{c}
       y_1 \\
       \vdots \\
       y_n
     \end{array} \right)
 \end{align*}
 $$

    \(\begin{align*} & \phi(x,y) = \phi \left(\sum_{i=1}^n x_ie_i, \sum_{j=1}^n y_je_j \right) = \sum_{i=1}^n \sum_{j=1}^n x_i y_j \phi(e_i, e_j) = \\ & (x_1, \ldots, x_n) \left( \begin{array}{ccc} \phi(e_1, e_1) & \cdots & \phi(e_1, e_n) \\ \vdots & \ddots & \vdots \\ \phi(e_n, e_1) & \cdots & \phi(e_n, e_n) \end{array} \right) \left( \begin{array}{c} y_1 \\ \vdots \\ y_n \end{array} \right) \end{align*}\)