$re = '/(?:#include ".*?|(?<!^)\G.*?)\KFoo/m';
$str = '#define Foo
#include "abcFoo1/Foo123/aFoo"
int Foo = 69
';
$subst = "Bar";
$result = preg_replace($re, $subst, $str);
echo "The result of the substitution is ".$result;
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php