I was also having issues installing mcrypt on my VPS dev server so I thought I would post my solution in the hopes that it helps someone. I am running Centos OS 6.5 and had upgraded PHP to 5.5.13 using the Webtatic EL yum repository. https://webtatic.com/packages/php55/
First shh into your server
ssh [email protected]
initially I was trying to do (which was not working):
yum update
yum install php-mcrypt
I then realized my mistake when I looked at php -v and realized php-common was conflicting as the above code was trying to load a dependency from 5.3.
I then executed the following correct commands:
rpm -Uvh http://mirror.webtatic.com/yum/el6/latest.rpm
yum update
yum install php55w-mcrypt
service httpd restart
This worked perfectly for me.
I also read while researching this issue that some people did have to add the extension to their .ini file manually by adding the following line but i did not have to do this.
extension=mcrypt.so
you can find the location of your php.ini file by looking at phpinfo(); and see which configuration it is loading. For me the following ini files were loading:
/etc/php.ini
/etc/php.d/mcrypt.ini
/var/www/vhosts/system/domain.com/etc/php.ini
If the installation is successful then you will see the extension when you echo phpinfo();

phpinfo()ORphp -i | head- Diemuzi