If the pain is unbearable after just two to three minutes then you may have overdone it and injured something. What kind of guitar are you playing? Acoustic or electric. Acoustic will be much harder due to thicker strings that are under more tension to create the sound. Electrics are easier but offer some other drawbacks. Whichever you have you can have the guitars "action" distance between string and frets lowered so you don't have to press down so much. Also put some lighter guage strings on. Ernie Ball makes a nice light gauge but any brand that says 9 or 10 on them would work better for you. The guitar shops have techs that can do all this for you. It's part of a "setup" usually around 40-50 dollars. Or there is an online guitar tech on this site who can help you. He has many tips on here on how to do this yourself if your willing. His name is Stephen White. Go to the home screen and scroll down to the bottom and you'll see his thread.

Also I went through a lot of this myself so I'm just basically telling you what was passed on to me. If everything above checks out and you feel there is something else causing it you could try asking some of the instructors. It could be the way your fretting the notes. Maybe pressing down too hard or not placing the fingertip properly behind the fret. These are all things that are covered in Fundamentals one. Beginners have a tendency to grip too hard when first learning something. I still do it from time to time. Just relax and follow the instructors advice on proper fretting and hand / finger position.

Good Luck,

Moe