Please note, this method should be a last result for users who cannot delete emails through one of the Webmail clients:

Mass Delete Emails in Horde
Mass Delete Emails in Roundcube
Mass Delete Emails in SquirrelMail

If you have tried using a Webmail client but are experiencing issues deleting messages, you can delete the folders that make up the Inbox by using the cPanel File Manager. Please keep in mind that with this method, there is no opportunity to view any of the messages before deleting them.

Log into your cPanel Account.

Click on the File Manager icon and choose "Home Directory" in the pop up window.

Navigate to the mail folder inside your home directory (/mail).

Under the mail folder, go into the folder with the domain name of the email account (after the @ symbol in the email address).

In the domain name folder, go into the email user name folder (the part of the email address before the @ symbol).

Select the "cur" and "new" folders and select "Delete" from the menu at the top of the screen.

This may take several minutes to complete, depending on the size of the folders.

As soon as a new email message is received in your email account, both the "cur" and "new" folders will be recreated in your account.