To install IonCube, you first need to download and extract the files:

wget http://downloads3.ioncube.com/loader_downloads/ioncube_loaders_lin_x86-64.tar.gz
tar xvfz ioncube_loaders_lin_x86-64.tar.gz

Next you will need to copy the files into your PHP extension directory. This will be different on different distros and with different PHP versions. So to find it, run:

php -i | grep extension_dir

The output will be similar to:

extension_dir => /usr/lib/php5/20121212 => /usr/lib/php5/20121212

Now copy the IonCube file matching your PHP version to that directory. You can do so with:

PHP_VERSION=$(php -r "echo PHP_MAJOR_VERSION.'.'.PHP_MINOR_VERSION;")
sudo cp "ioncube/ioncube_loader_lin_${PHP_VERSION}.so" /usr/lib/php5/20121212/

Then, in order for FPM to correctly find the extension, create a file named /etc/php5/fpm/conf.d/00-ioncube.ini with the contents:

zend_extension = /usr/lib/php5/20121212/ioncube_loader_lin_5.5.so

Finally, restart PHP-FPM using service php5-fpm restart