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The CloudFlare cPanel plugin makes it easy to integrate into your hosting control panel. It takes less than 5 minutes to install on a test server and then the service is available to your end customers with two clicks.

Before proceed to install cloudflare plugin, you should get HOST KEY from cloudflare partners 

https://www.cloudflare.com/certified-partners

Installation

Install cloudflare cpanel plugin Using an SSH client such as Terminal or Putty:

Step 1. Access cPanel for the server using root user by:

ssh root@SERVER IP ADDRESS or SERVER NAME

Step 2.

cd /usr/local/cpanel

Step 3.

curl -k -L https://github.com/cloudflare/CloudFlare-CPanel/tarball/master > cloudflare.tar.gz

Step 4.

tar -zxvf cloudflare.tar.gz

This extracts a directory that includes a UNIQUE ID. For example, the directory will be in this format:
cloudflare-CloudFlare-CPanel-d03f3b8
The UNIQUE ID is only: d03f3b8
The UNIQUE ID is not cloudflare-CloudFlare-CPanel-d03f3b8

Step 5.

cd cloudflare-CloudFlare-CPanel-UNIQUE ID/cloudflare/

Step 6.

./install_cf API HOST KEY mod_cf “YOUR COMPANY NAME”

example for Awesome Hosting Company: ./install_cf 56yt8x9s987dfy4324bnv mod_cf “Awesome Hosting”

Step 7. This will start the installation. cPanel is installed first, followed by mod_cloudflare. Depending on your server, it will take between 15 seconds and 4 minutes. You know it will be done when you see:
CloudFlare module installed successfully

Step 8. CloudFlare is now successfully added to this server. You need to repeat the process for each additional server (unless you have an automatic update script).

Best SysAdmin practices

Now that CloudFlare is installed, you can remove some of the unnecessary remnant files:

Step 9.

cd ../ ../

This takes you back two levels.

Step 10.

rm -rf cloudflare-CloudFlare-CPanel-UNIQUE ID*

To check if it is installed:

cat /etc/cloudflare.json
or
cat /usr/local/cpanel/etc/cloudflare.json

You should see an output with the following:

root@server1 [/usr/local/cpanel]# cat etc/cloudflare.json
{
 “host_key”:”32yt5a7b436tuy8974tre -”, (For security purposes, this will not be your host key.)
 “host_formal_name”:”Awesome Hosting”,
 “host_name”:”api.cloudflare.com”,
 “host_uri”:”/host-­gw.html”,
 “user_name”:”www.cloudflare.com”,
 “user_uri”:”/api_json.html”,
 “host_port”:”443”,
 “host_prefix”:”cloudflare-­resolve-­to”,
 “cp_version”:”1.3.0”
}

Uninstall:

/usr/local/cpanel/bin/unregister_cpanelplugin /usr/local/cpanel/3rdparty/cloudflare.cpanelplugin

Test Websites

To ensure that CloudFlare was properly installed, enable CloudFlare for three test websites from your control panel.

To check if a website is on CloudFlare, use Terminal. Open Terminal, and enter the following dig command.

dig www.mydomain.com<

Output without CloudFlare-enabled:

www.mydomain.com 10782 IN CNAME www.mydomain.com

Output with CloudFlare-enabled:

www.mydomain.com 10782 IN CNAME
www.mydomain.com.cdn.cloudflare.net.

If you see ‘.cdn.cloudflare.net’ at the end, then CloudFlare is enabled.