This article is for cPanel Accounts. Determine where your account is with this guide.
Web servers often have a CGI-bin/ directory at the base of their directory tree to hold executable files called CGI. A CGI-bin is a special directory designated in the configuration files of a web server to allow the execution of CGI scripts in specified directories. Many new servers have done away with this and allow users to execute any scripts ending in .CGI.
The CGI-bin/ remains as a default folder on all new accounts. This is simply to remain compatible with older scripts. If you do not intend to use the CGI-bin, it can be deleted without any problem. It can be easily re-created as well, just by re-making the directory.