Remove the cranks, take out the bottom bracket. Clean off all the threads. Grease all the threads. Reassemble everything. Shouldn't click. No harm doing this first, as you should be doing it regularly anyway.

If it still clicks. Check the handlebar/stem interface. Loosen the faceplate of the stem, rotate the bars down and then back up, tighten everything back up and see if it stops clicking.

Hopefully this does it. These are the parts that click the most on my bikes. If it still clicks, then maybe take it to a bike shop and ask their opinion. Sounds travel up and down the frame of the bike and often aren't in the place where they seem to be coming from.