No, it works correctly. But you need to handle the encoding appropriately: tell Perl what encoding is used on input (binmode on *DATA below), what encoding is used in the source code (here utf8), and what encoding is used on output (binmode on *STDOUT). Configure the terminal to use the output encoding.

#!/usr/bin/perl
use warnings;
use strict;
use utf8;
use feature qw{ say };

binmode *STDOUT, ':encoding(UTF-8)';
say substr('Ĉon Flux', 0, 1);

binmode *DATA, ':encoding(UTF-8)';
say substr <DATA>, 0, 1;

__DATA__
Ĉon Flux
[download]

Output:

Ĉ
Ĉ
[download]