Combine the water and sugar in a saucepan and bring to a boil over medium-high heat. Let cook, stirring constantly, until the mixture becomes syrupy and bubbles approximately 3 minutes.
Reduce the heat to medium and add the fennel seeds to the syrup. Stir constantly until the mixture crystallizes. (This happens quickly -- the fennel seeds will look sort of dry).
Immediately remove from the heat. Stir a few more seconds until the fennel seeds are completely dry and separated.
Let dry completely at room temperature, then store in an airtight container until ready to use.
