Have a look at alarm. Timing out input is the example in the documentation.

Update: Code:

printf "Answer: %d\n", yn();

sub yn {
    my $question = shift;
    $question ||='Your answer? ';

    my $val = undef;

    until (defined $val){
        print "$question (y/n): ";
        eval {
            local $SIG{ALRM} = sub { die "alarm\n" };
            alarm 3;
            $val = <STDIN>;
            chomp $val;
        };
        if ($@) {
            die $@ if $@ ne "alarm\n";
            warn "No answer for three seconds.\n";
            $val = 'n';
        }
        # $val =
        #   $val eq 'y' ? 1 : (
        #      $val eq 'n' ? 0 : undef
        #   );

        if ($val eq 'y'){
            $val = 1;
        }
        elsif ($val eq 'n'){
            $val = 0;
        }
        else {
            $val = undef;
        }
    }
    return $val;
}
[download]

I tried this a couple times. If I don't answer, it looks like this:

Your answer?  (y/n): No answer for three seconds.
Answer: 0
[download]

...and that takes three seconds.

With an answer, it looks like:

Your answer?  (y/n): y
Answer: 1
[download]