Unfortunately, there is no Ghost support for footnotes yet in Markdown.
However, a user on the Ghost community forum has provided a HTML-based solution for footnotes.
The sentence leading up to the notation.<sup><a href="#fn1" id="ref1">1</a></sup>
<sup id="fn1">1. Here is the notation that the sentence above leads up to.<a href="#ref1">↩</a></sup>
Quite useful, I have to say.