On Unix-like operating systems, the output of the command is slightly different from $USER because whoami outputs the username that the user is working under, whereas $USER outputs the username that was used to login. For example, if the user logged in as John and su into root, whoami displays root and echo $USER displays John. This is because the su command does not invoke a login shell by default.
The earliest versions were created in 2.9BSD as a convenience form for who am i, the Berkeley Unix who command's way of printing just the logged in user's identity. The GNU version was written by Richard Mlynarik and is part of the GNU Core Utilities (coreutils).
This command was also available as a NetWare-Command residing in the public-directory of the fileserver. It also outputs the current connections to which server the workstation is attached with which username.