Wkhtmltopdf does support even very complex headers and footers.
wkhtmltopdf.exe -T 50mm --header-html www.google.com www.stackoverflow.com test.pdf && test.pdf
That command uses the page at www.google.com as a 50mm header for www.stackoverflow.com for every page.
Note: If you use a custom page for the header/footer, you need to add <!DOCTYPE HTML> in the beginning of your header/footer HTML!