Before starting you should:

• Have WinSCP installed;
• Know how to connect to the server without public key authentication.

If you do not have a key pair yet, start with generating new key pair.

Connect to your SSH server using WinSCP with the SSH protocol, using other means of authentication than public key, e.g. typically using password authentication.

Once logged in, configure your server to accept your public key. That varies with SSH server software being used. The most common SSH server is OpenSSH.

You can use Session > Install Public Key into Server command on the main window, or Tools > Install Public Key into Server command on SSH > Authentication page page on Advanced Site Settings dialog. The functionality of the command is similar to that of OpenSSH ssh-copy-id command.

Or you can configure the key manually:

• Navigate into a .ssh subdirectory of your account home directory. You may need to enable showing hidden files to see the directory. If the directory does not exists, you need to create it first.
• Once there, open a file authorized_keys for editing. Again you may have to create this file, if this is your first key.
• Switch to the PuTTYgen window, select all of the text in the Public key for pasting into OpenSSH authorized_keys file box, and copy it to the clipboard (Ctrl+C). Then, switch back to the editor and insert the data into the open file, making sure it ends up all on one line. Save the file. WinSCP can show you the public key too.
• Ensure that your account home directory, your .ssh directory and file authorized_keys are not group-writable or world-writable. Recommended permissions for .ssh directory are 700. Recommended permissions for authorized_keys files are 600. Read more about changing permissions.

• Save a public key file from PuTTYgen, and copy that into the .ssh2 subdirectory of your account home directory.
• In the same subdirectory, edit (or create) a file called authorization. In this file you should put a line like Key mykey.pub, with mykey.pub replaced by the name of your key file.

For other SSH server software, you should refer to the manual for that server.

When configuring session, specify path to your private key on SSH > Authentication page of Advanced Site Settings dialog.

Alternatively, load the private key into Pageant.

Cloud providers have typically their own mechanism to setup a public key authentication to virtual servers running in the cloud.

For details see guides for connecting to:

• Amazon EC2;
• Google Compute Engine;
• Microsoft Azure.

• Using Public Keys for Authentication;
• Using PuTTYgen;
• Understanding SSH Key Pairs.