Run an ssh shell to your server.
Run the following command:

cd /usr/local/src/
git clone
cd letsencrypt/
./letsencrypt-auto --help all

Now login to your webmin admin panel at:
https://siteaddress:10000/ using root username.

Webmin configuration>SSL Encryption>Let’s Encrypt

It will show you:

Let's Encrypt is a free, automated, and open certificate authority that can be used to generate an SSL certificate for use by Webmin.
Unfortunately, Let's Encrypt cannot be used on your system : The client command letsencrypt was not found on your system.
Check the module configuration page to ensure you are using the correct path to the letsencrypt or letsencrypt-auto command.

Click on “module configuration”
and type in the path and click Save:

For module Webmin Configuration
Full path to Let's Encrypt client command: /usr/local/src/letsencrypt/letsencrypt-auto

To enable SSL certificate for a site, Go to:
Virtualmin>Edit Virtual Server>Enabled features

Enable “SSL website enabled”

To Manage the certificate:
Virtualmin>Server configuration>Manage SSL certificates

Click on Letsencrypt and generate a new certificate