It isn’t rare for PEers to experience pain in their favorite organ. Are you jelqing at a high % erection, maybe?
I’ve read through several threads in the injury forum relating to pain associated with jelqing. I found several describing a sharp pain on the right side of the penis, usually being around the glans or along the shaft itself (again, for some reason, often on the right side).
Sometimes I have slight pain at the base, and also pain near the glans, but I can’t remember if it happens in the same fashion as yours: starting at the base, skipping mid-shaft, and then appearing around the glans. It’s been a while since I’ve felt pain, as I tend to be a very cautious PEer. Try taking it easy for a bit, as in a less vigorous workout, or maybe even a day or to off, and then restart with a less vigorous workout.
"Only enemies speak the truth; friends and lovers lie endlessly, caught in the web of duty". -Roland, in Stephen King's The Last Gunslinger