One of the meanings of "funny" is odd, unusual, extraordinary, freakish, strange, uncommon, ... So, "funny you should ask" means "how odd it is that you should ask". The reason it is odd because of the extraordinary coincidence, as explained by Adrian and DavidK.

As DavidK says, it expresses surprise that the topic has come up. It is often followed by an explanation for the listener : ‘I was just thinking about that’, for example.

‘Funny you should ask’ suggests some kind of coincidence- you were recently thinking about the question or learned something about the question before the question was asked. Funny= what a coincidence that