"Github pages" hosts web page from index.md / readme.md as main page . However if you have an index.html file then it'll be hosted from html file.However , if you are trying to host a multi page website using "Jekyll themes" then Jekyll theme is not straightaway deployed in subsidiary pages .
Case 1) You are using markdowns to host your pages
index.md -> main page
page1.md -> page 1 of your website
..
so on
To generate a multiple page website using github page just give relative path to the required page without extension i.e.
make a button
<a href="./page1">Go to next page</a>
And by clicking on this button you will be directed to page1 with jekyll theme deployed