How long will joint pain last after taking doxycylcine hydate? I took the medication 2 times a day for seven days for chlamydia. After taking a single dose of antibiotics, the std did not go away. So I waited about three months or more and tested positive for Chlamydian again. So the Dr. prescribed me doxyxylcine. On a couple of occasions, mostly morning, I had nausea. One of the mornings I went to grab the remote and got an alarming pain in my left elbow on both sides of the joint (bicep/tricep). And it has continued to spread throughout my other joints on both sides: knees, knuckles, and elbows. I stopped taking the medication on 5-28-14. I d like to know what s the usual recovery time from this side effect if at all? I work out and I have had to stop all activity due to this problem.