Well, we had the same issue with our house. And here's what we did:

We snaked new cables in the wall for the fan, and we bought and installed a new light switch that has a timer on one side, and a normal switch on the other. We had to enlarge the wall to fit this bigger switch, and we had to make all the relevant connections with the cables. It was actually fairly easy, surprisingly. Of course, I did that with someone that has over 35 years of experience working in the construction industry, so your mileage may vary.