Command line to remove an environment variable from the OS level configuration

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To remove the variable from the current environment (not permanently):

set FOOBAR=

To permanently remove the variable from the user environment (which is the default place setx puts it):

REG delete HKCU\Environment /F /V FOOBAR

If the variable is set in the system environment (e.g. if you originally set it with setx /M), as an administrator run:

REG delete "HKLM\SYSTEM\CurrentControlSet\Control\Session Manager\Environment" /F /V FOOBAR

Note: The REG commands above won’t affect any existing processes (and some new processes that are forked from existing processes), so if it’s important for the change to take effect immediately, the easiest and surest thing to do is log out and back in or reboot. If this isn’t an option or you want to dig deeper, some of the other answers here have some great suggestions that may suit your use case.

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