should work. This has nothing to do with how perl executes it, but everything with how the shell does it - if you type the contents of the system call in the shell you get the same behaviour.

You could also open a pipe, and write to it:

open my $at, '|-', 'at', qw(now + 1 minute)
   or die "can't open pipe to 'at': $!";
print $at "rm $session_file";
close $at or die $!;
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Or you could use CGI::Session which handles session timeouts for you in a transparent way.