Foot overpronation is associated with an increased risk for patellofemoral pain in runners. For this reason, foot orthotics can be used to treat patellofemoral pain in runners.
However, the link is not that strong and there are many other factors involved.
The model that this is traditionally based on is that as the foot pronates, the tibia internally rotates and this affects the alignment at the knee. If the foot overpronates, then this malignment is excessive and can cause problems, especially if activity levels are high. The evidence is not actually that good at supporting this model and it is not necessarily exactly what happens and it is very complex.
The preponderance of the prospective evidence does show that foot “overpronation” does increase the risk for patellofemoral pain. Given the evidence on the mechanism above is mixed, it is possible that it affects the knee via other mechanisms.