Certainly. Something like the following:

#!/usr/local/bin/perl

use feature qw/say/;
use strict;
use warnings;

open my $FASTAFILE, "<", 'human_fold_25.txt'
    or die "Could not open file: $!";

my $sequence = ' ';
my $Ccount = 0;
my $Gcount = 0;
my $identifier = ' ';

while(my $line = <$FASTAFILE>) {

    chomp $line;
    next if $line =~ m/^\./;

    if ($line =~ /^>/) {
        $identifier = $line;
    } elsif ($line !~ /^\(/) {

        $sequence = $line;
        $Gcount = $Ccount = 0;

        my $sequencelength = length $sequence;
        my @nucleotides = split('', $sequence);

        foreach my $nuc (@nucleotides) {
            if ($nuc eq 'G') {
                $Gcount = $Gcount + 1;
            } elsif ($nuc eq 'C') {
                $Ccount = $Ccount + 1;
            }
        }

        my $GCcontent = ((($Gcount + $Ccount) / $sequencelength) * 100
+);
        say "$identifier, $GCcontent";

    }
}

close $FASTAFILE or die "Could not close file: $!";
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Note I've made a few other changes to your code, namely:

• use strict;, and use warnings;. These are your friends; they'll catch many errors for you, and you should always use them. As a side effect, I've also declared variables with my where necessary.
• use feature qw/say/; it's nicer than print if you want to add a newline anyway, IMO.
• Lexical filehandles ($FASTAFILE vs. FASTAFILE).
• Three-argument form of open.
• Error checking for open and close.
• Slightly more idiomatic handling of lines starting with periods.
• Whitespace changes, to improve readability.

Your code could still be tightened up further, of course. For instance, the entire block following elsif ($line !~ /^\(/) could be reduced to the following:

    ...
    } elsif ($line !~ /^\(/) {

        my $GCcount =()= ($line =~ m/(G|C)/g);
        say "$identifier, " , ($GCcount / length($line) * 100);

    }
    ...
[download]

but since you're still new to Perl, I imagine that wouldn't make as much sense. :)