If you are using CGI.pm, you can provide the path to your .js file while you list the other "head elements" (eg title etc.)...something like this...

#c:\perl\bin\perl
use CGI qw/escape unescape/;
$query = new CGI;
#########################################
print $query->header();
#########################################
#send javascript functions into head
#You can include external style sheets, javascript , metatag info etc
print $query->start_html(-title => 'Place page title here', -script=>{
+-language=>'javascript', -src=>'path to
->/javascript/functions.js'});

#########################################
#Put your html output here and you are good to go!!!!!
#########################################
#Finish CGI.pm Output
print $query->end_html;
#########################################
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