I've not done so, but I don't see why not. You'll need to use more - 3 to 4 teaspoons of fresh leaves depending on how much thyme flavor you want. If you try it, let me know how it works so I can edit the recipe in the future.

Gingerroot reported making it with fresh thyme, in the comments. I have made it with dried, and I love it and look forward to keeping this around all summer.

Agree with the above. I still have popsicle freezer molds I used with the son and the daughter when they were little. They make great adult ice sicle tea molds.