Remove row from system table with hook_update_N
I think your code should look something like this:

&lt;?php

/**
 * Delete row from system table.
 */
function MODULENAME_update_7001() {
  db_query('DELETE FROM {system} WHERE name = :name', array(':name' =&gt; 'FOO'));
}


This should go in the MODULENAME.install file of your module. Of course you'll need to replace MODULENAME with the name of your module and FOO with the name of the row you want to delete.

Relevant documentation can be found at Updating tables: hook_update_N() functions, hook_update_N and Database abstraction layer.