It won't. http://stackoverflow.com/a/28457335/239657 http://stackoverflow.com/a/28457335/239657 (1) Last I checked, cloudflare's "Strict SSL" mode only accept

It won't. http://stackoverflow.com/a/28457335/239657 http://stackoverflow.com/a/28457335/239657 (1) Last I checked, cloudflare's "Strict SSL" mode only accepts from the backend a cert for the custom domain you're trying to serve, not accepting the github.io cert. A pity they don't let me configure what cert(s) to accept from the backend... (2) In addition, Github have indicated their current github.io SSL is not actually end-to-end secure — it's only secure from their CDN (Fastly) but their link to the CDN is unsecure. So there is absolutely zero you can do — Cloudflare or anything else — to make GH Pages end-to-end secure on custom domains.