When i run the back of my knee kinda hurts when i bend my knee. what could be going on?

Internal derangement: Internal derangement of the knee covers a broad spectrum of underlying damage. A swollen knee will hurt in the back as the pressure sensitive pain fibers of your knee capsule (mostly in the back) send a pain signal to your brain with increased loading of the joint. Cartilage damage, a meniscus tear are most common culprits. Orthopaedic evaluation, standing xrays, and possible MRI are warranted.