By adding use strict, fixing the errors flagged by strictures, fixing the indentation and using Perl rather than C I get the following (which may or may not do what you want):

#!usr/bin/perl
use warnings;
use strict;

my $ntotal;

for (1 .. 5000) {
    my $k     = 25;
    my $N     = 10000;
    my @cls;
    my $total = 0;

    while ($k >= 2) {
        my $mean = (4 * $N) / ($k * ($k - 1));
        my $time = (-log (rand) * $mean);

        $ntotal += $time;
        push @cls, $time;
        --$k;
    }

    my $nmean = $ntotal / 5000;
    print "$nmean\n";
    
    my @low = grep {$_ <= $nmean} @cls;
    my $nLow = scalar @low;
    my $hig = scalar (5000 - $nLow);

    print "$nLow\n";
    print "$hig\n";
}
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Prints:

2.37332066086488
0
5000
6.21051651542152
1
4999
8.59464183062829
0
5000
...
[download]