If you are using GD::Graph then see use_axis=>[1,2] and two_axes=>1 in section "Options for graphs with axes".

#!/usr/bin/perl
use strict;
use GD::Graph::lines;

my $graph = GD::Graph::lines->new(400, 300);
$graph->set( 
      two_axes => 1,
      use_axis => [1,2],
      x_label  => 'X Label',
      y1_label => 'Y1 label',
      y2_label => 'Y2 label',
      title    => 'Some simple graph',
) or die $graph->error;

my @data = ([1,2,3,4,5], [2,3,4,5,6], [17,14,18,16,12] );
my $gd = $graph->plot(\@data) or die $graph->error;

open IMG, '>','file.png' or die $!;
binmode IMG;
print IMG $gd->png;
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