The simplest solution is to just include PHP code inside the <script></script> section of your HTML templates / web pages because chances are, the file extension is .php:
<script> var jsVar = "<?php echo $phpVar ?>"; </script>
Even if it’s not ending in .php, such as in .html or .htm, you can configure your server to parse all .html or .htm files for any PHP code, though with a little extra server burden.
Another solution for this is to make your server parse all files ending in .js. Just create a .htaccess if it doesn’t exist in the directory in which you wish to include and run PHP code inside all .js files. Add these lines at the end of .htaccess:
AddType application/x-httpd-php .js AddHandler x-httpd-php5 .js <FilesMatch "\.(js|php)$"> SetHandler application/x-httpd-php </FilesMatch>