I know you said you don't want to open it first, but I don't know if there is any other way to do it.

What if you did something like this? (untested):

use IO::Select;

open my $fh, "<", $fifo or die "couldn't open $fifo: $!";

my $sel = IO::Select->new($fh);
if ($sel->can_read(0.1)) {
    close $fh;
    do_database_stuff();
}
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