From:https://github.com/mojombo/jekyll/wiki/Usage

Note: Pagination does not work with markdown files, it only works with html file extensions.

Just follow these steps to add pagination to your blog:

_config.yml

add the pagination setting:

markdown: rdiscount
pygments: true
lsi: true
exclude: ['README.markdown', 'README_FOR_COLLABORATORS.markdown', 'Gemfile.lock', 'Gemfile']
production: false
//add this line to add pagination
paginate: 3 //the number of post per page

index.html

just add the posts and the pagination links:

---
layout: default
title: Blog
---


   
<!-- Pagination links -->
<div class="pagination">
  
    <span class="previous">Previous</span>
  
  <span class="page_number ">Page:  of </span>
  
    <span class="next ">Next</span>
  
</div>

A note about page1

Jekyll does not produce a page1 folder so using the above code will not work when a link is produced of the form “/page1”. The following textile will handle page1 and render a list of each page with links to all but the current page.

<div id="post-pagination" class="pagination">

  
  <p class="previous disabled">
    <span>Previous</span>
  </p>
  

  <ul class="pages">
    <li class="page">
      
      <a href="/">1</a>
      
    </li>

    
  </ul>

  
  <p class="next disabled">
    <span>Next</span>
  </p>
  

</div>