Could be a number of things, though most likely it's either the master cylinder, slave or hydraulic line between the two. I'd start by checking the fluid level in the reservoir on the master cylinder. It's in the engine bay, driver side on the firewall (near the brake fluid reservoir). It has a small black cap. If it's empty / low then you probably have a leak somewhere. If the leak is at the master you should see evidence of this just looking at it / around it. If everything looks good with the master, the leak is at the slave or in the line somewhere in between the two. Luckily on 94 and later models the slave is mounted externally on the bell housing so it's relatively easy to access / replace. Believe it's on the driver side of the bell housing, just trace the hydraulic line down from the master until you find it. Once you find it you may actually have to remove it to see if it's leaking. If you've checked everything and can't find an obvious leak, add some fluid to the reservoir (if empty/low) and have someone pump the clutch while you trace the system from master down to slave looking for leaks. If everything is good (or you have plenty of fluid in the reservoir to begin with) then check the slave. Again, after removing it from the bell housing have someone pump the clutch, you should see the piston on the slave extend as the clutch is depressed. If the piston in the slave is retracted and they press the clutch and nothing happens then the problem is with the slave and/or master. If everything appears to be working properly then the problem is probably elsewhere (broken clutch fork possibly). If it's just the master or slave cylinder it's a relatively easy job.
P.S.- I'd move your post to the YJ model tech forum if I were you. Probably be able to get some input from folks who've had the same problem (not that I haven't been in your shoes, but it was with a Jetta).