The following steps will help you create a custom php.ini file for a cPanel account when using CGI or FCGI as the PHP handler.

Enter to the cgi folder.

cd /home/user/public-html/cgi-bin

Copy the php.ini to that folder

cp /usr/local/lib/php.ini /home/user/public_html/cgi-bin

Open the php.ini

vi php.ini

Change the PHP variable

For Example: register_globals = On

Create php.cgi (under the /home/user/public-html/cgi-bin folder) file to load custom php.ini, with the following content:

#!/bin/sh
/usr/local/cpanel/cgi-sys/php5 -c /home/user/public_html/cgi-bin/

Please note the path to php5 is due to using PHP5 on this system. If you are using php4, it might be /usr/local/cpanel/cgi-sys/php4 or some other path. Check /etc/httpd/conf/php.conf to see what it shows for the cgi-sys path for your version of PHP.
Save the file, then made executable:

chmod +x /home/user/public_html/cgi-bin/php.cgi

Change ownership of files to correct user:

chown -R user:user /home/user/public_html/cgi-bin/

Go to the document root and edit .htaccess to point to php.cgi wrapper

cd /home/user/public_html
vi .htaccess

Put the code given below at the top of the file:

Action application/x-httpd-php5 /cgi-bin/php.cgi

Again, here php5 is listed. If your PHP is different, use the Action listed for your version of PHP in /etc/httpd/conf/php.conf file.

So that’s how you create a custom php.ini file when the handler is CGI or FCGI in cPanel.