GCC fatal error: stdio.h: No such file or directory

macOS

I had this problem too (encountered through Macports compilers). Previous versions of Xcode would let you install command line tools through xcode/Preferences, but xcode5 doesn't give a command line tools option in the GUI, that so I assumed it was automatically included now. Try running this command:

xcode-select --install

If you see an error message that developer tools are already installed (and still header files can't be found), wipe out any existing one to do a fresh installation:

sudo rm -rf /Library/Developer/CommandLineTools

Ubuntu

(as per this answer)

sudo apt-get install libc6-dev

Alpine Linux

(as per this comment)

apk add libc-dev

Mac OS Mojave

The accepted answer no longer works. When running the command xcode-select --install it tells you to use "Software Update" to install updates.

In this link is the updated method:

Open a Terminal and then:

cd /Library/Developer/CommandLineTools/Packages/
open macOS_SDK_headers_for_macOS_10.14.pkg

This will open an installation Wizard.

Update 12/2019

After updating to Mojave 10.15.1 it seems that using xcode-select --install works as intended.

ubuntu users:

sudo apt-get install libc6-dev

specially ruby developers that have problem installing gem install json -v '1.8.2' on their VMs