Via the page Git Submodule Tutorial :

To remove a submodule you need to:

  1. Delete the relevant section from the .gitmodules file.
  2. Stage the .gitmodules changes:
    git add .gitmodules
  3. Delete the relevant section from .git/config.
  4. Remove the submodule files from the working tree and index:
    git rm --cached path_to_submodule (no trailing slash).
  5. Remove the submodule's .git directory:
    rm -rf .git/modules/path_to_submodule
  6. Commit the changes:
    git commit -m "Removed submodule <name>"
  7. Delete the now untracked submodule files:
    rm -rf path_to_submodule

See also : alternative steps below.