This is a common thing, and in most cases, easy to fix.
Incline on the treadmill puts more stress on the lower back
When walking or running uphill, the load on the muscles change. You are forced to lean forward, your back muscles have to compensate a lot more to keep you erect. The hip flexors also have to work more, because you need to lift your knees higher. The psoas consequently exerts a stronger forward pull on your low back. Your stride also gets shorter and quicker, therefore your muscles get tired more quickly. The result is compression of the lower back, which can result in pain.
How to get rid of the pain
- Give yourself more time to adapt. Reduce the incline. Walk, not run uphill first, so there is less impact. You can even hold onto the treadmill.
- Get some form of strength training. Weighted squats, bench step-ups are the best candidates, as they target the very same muscles which get more stress running uphill.
- More flexibility will also help. Tight hamstrings, calves, low back muscles increase the likelihood of pain. In addition, I would also specifically stretch out hip flexors after an incline treadmill session, tightness in that area can easily develop into lower back pain later.