I had a hair transplant last year and I can say from my experience that yes, there is some discomfort during the procedure. The anesthesia injections can be a bit painful, but once that kicks in, you shouldn't feel much during the actual transplant. Recovery for me wasn't too bad either - there was some soreness and swelling for the first few days, but it was manageable with pain medication.
Overall, I would say the discomfort during the procedure and recovery was worth it for the results I got. Just make sure to follow your doctor's post-op instructions and give yourself time to heal properly. It's a big decision, but if you're unhappy with your hair loss, it can be a life-changing one.