A long, long time ago I asked a question - this is the answer!
Qlikview over SSL /w Windows Server 2008 / QlikView v9, v10, v11 / Using QlikView Web Service (not IIS).
In these instructions substitute "fqdn" with the fully qualified domain name you've registered your SSL certificate against.
Configure AccessPoint for SSL
1. Follow the QlikView Server/Publisher Reference Manual appendix section 40
(How to Activate SSL for Services in Windows) to bind the certificate to port 443
Change all config.xml files to use HTTPS instead of straight HTTP, then restart the QlikView services.
<HttpAuthentication url="https://_/scripts/GetTicket.asp" scheme="Basic" />
Save the changes to the config files and restart the QlikView Web Server service.
Users should now only be able to browse to the https version of the AccessPoint URL, e.g.
Configure QEMC for SSL
1. Bind the certificate to port 4780 using the same approach as for the AccessPoint, e.g.
netsh http add sslcert ipport=0.0.0.0:4780...
2. Edit the QlikView Management Service config file [QVManagementService.exe.config] found in the default location:-
[C:\Program Files\QlikView\Management Service]
3. Modify the "UseHTTPS" to "true" and save the config file.
4. Restart the QlikView Management Service.
5. QlikView admins should now only be able to browse to the https version of the QEMC URL (Start menu link will no longer work), e.g.
6. Ensure you can still configure the QVWS/AccessPoint settings under System > Setup > QlikView Web Servers > QVWS@
From what I'm aware, you need to do it via IIS.
You have to have Qlikview installed using IIS as the webserver.
Then once you've installed Qlikview and open IIS, you'll see the Qlikview website appear under IIS as Default website.
Load the SSL certificate on the site and then enable SSL.
This should work, but I'm still struggling to deploy across the web (ie, not on the same domain)
You can do it either by using QVWS or IIS, both options are possible.
If you're familiar with IIS then it might be easier to setup. I'm not sure what you meant with "Since this site isn't a typical website (there's no website in IIS)" but it is a typical website, you will see it in IIS as the default website or as the one you selected when you did the installation.