You do a bit of extra hocus here, and your justification of the /s modifier to your regex isn't quite right.

$marker = "<!-- NEW URL HERE -->";

# let's use perl's built-in in-place editing
# please check the 'perlrun' documentation for
# explanation of the -i switch, and the 'perlvar'
# documentation for the corresponding $^I variable

{
  # $^I = "" <-- no backup file
  # @ARGV = ("foo.html") <-- magical <> works on this file
  local ($^I, @ARGV) = ("", "foo.html");

  while (<>) {
    # \Q will escape any special regex chars in $marker
    # if any exist -- good safety measure!
    s/\Q$marker/$url<BR>\n$marker/;
    print;
  }
}
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If you want to be a sneaky little guy, you could use a positive look-ahead assertion, to avoid having to substitute $marker with something AND $marker:

    # stick "$url<BR>" RIGHT BEFORE $marker
    s/(?=\Q$marker)/$url<BR>\n/;
[download]

Yadda yadda.