Full Disclosure: I am NOT an expert at Jupyter or Anaconda (which I am using in this project), there may be some bad habits below...
Below is a quick scratchpad of the steps I took to serve Jupyter from a subdomain. Jupyter is running behind NGINX on an OpenStack Ubuntu instance and the domain's DNS is set up to use Cloudflare to provides convenient SSL support. I was suprised by the lack of documentation for this process, prompting me to document my steps taken here.
Set up Cloudflare account, utilizing its provided Name Servers with my domain registration.
Set up Cloudflare DNS Record for subdomain (ex jupyter to server from jupyter.mydomain.com). In the image below, the DNS entry for the Jupyter server was "greyed-out", relegating it to "DNS Only" rather than "DNS and HTTP Proxy (CDN)".. Now that Cloudflare supports websockets, this is no longer necessary and you're able to take advantage of using Cloudflare as a CDN (admittedly, I'm not sure how useful this actually is, but it's worth mentioning).
Ensure Crypto settings are set correctly. You should probably be using Full SSL (Strict) rather than Flexible SSL as shown in the image below, however that is outside the scope of this post.