Use -p flag to run your code in the loop: 
 LINE:
                while (<>) {
                    ...             # your program goes here
                } continue {
                    print or die "-p destination: $!\n";
                }

[download]
and -i flag to edit files in-place (see perlrun for more). Use $. to check the line number. Define BEGIN{} to read the header, then write it in the main loop: 
perl -pi -e'BEGIN{$HEAD=shift@ARGV;open(HEAD);$main::head=<HEAD>}$_=$m
+ain::head.$_ if $.==1' header-file file-to-be-edited

[download]
Perhaps avoiding the -p will be more efficient, but not so compact: 
perl -e'($HEAD,$FILE)=@ARGV;open(HEAD);open(FILE);open($f,">$FILE.$$")
+;print $f scalar <HEAD>,<FILE>;rename "$FILE.$$","$FILE"' header-file
+ file-to-be-edited

[download]
Warning: both of the one-liners use somewhat deprecated one-argument open and barewords as filehandles.
Sorry if my advice was wrong.

In reply to Re: Single line insert to the start of a file by aitap
in thread Single line insert to the start of a file by darklord_999

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