Need more information… The type of rehab, stretching, and strengthening you do will depend on where the pain is and what tissue(s) are involved. As was mentioned above, Runner’s Knee broadly defines PFPS - patellar femoral pain syndrome which has many different underlying causes. IT band, muscle imbalance, Patellar Tendon, Quad Tendon, Patellar tracking problems (usually the end result of a tendon or muscle problem), even arch collapse throwing off your kinetic chain as you hit higher milage (read: form deteriorating as you get tired). They can all result in “Runners Knee”.
Generally speaking - overuse injuries will continue to get worse if you try to push through it. Once tendons and ligaments get inflamed, it can take some time for that to subside, and continual use will only make it worse. Blood flow to those areas is relatively poor, so it can take a long time to heal. My advice - with out knowing more specifics, is to rest, stretch, and restrict your work load to only those things that you can do pain free (during and after) for a week or so. Then slowly start adding in some running/cycling using pain as your guide. If it hurts, stop.