It could be that he's allergic to the jelly. There's quite a number of people who are allergic to certian types of condoms andd lubrications. With that in mind it's not alarming that he could be allergic, unfortuantely the way he and most people find this out is through use. Usually if you're going to use a lube for the first time it's a good idea to test it somewhere else (like your arm) to see if you're going to have some allergic reaction to it. Assuming that you've both know you're negative for STDs, and are monogamous it's probably just an allergic reaction. 

 Depending on the severity, you might have to be prescribed someting from your doctor. While not a fun conversation to have, they can write you up a prescription for  an ointment or some other form of medicaiton that will speed up healing time, and greatly reduce pain. In the meantime, you can talk to your local pharmacist, and they might be able to tell you what's good for skin allergies such as these. Remember, it's always a good idea to talk to youd doctor first before starting any form of treatment.

Hopefully he feels better soon! good luck!