The immunosuppressive mammalian target of Rapamycin (mTOR) inhibitors can cause proteinuria, especially in kidney and heart transplanted patients. Podocytes play a major role in establishing the selective permeability of the blood-urine filtration barrier. Damage of these cells leads to proteinuria, a hallmark of most glomerular diseases. Interestingly, podocyte damage and focal segmental glomerulosclerosis (FSGS) can occur after treatment with an mTOR inhibitor in some transplant patients. To investigate the mechanisms of mTOR inhibitor induced podocyte damage we analyzed the effect of Rapamycin on mTOR signaling and cellular function in human podocytes. We found that prolonged Rapamycin treatment reduced the expression of total mTOR, which correlates with diminished levels of mTOR phosphorylation at Ser2448 and Ser2841. In addition, treatment with Rapamycin reduced Rictor expression and mTORC2 formation, resulting in a reduced phosphorylation of AKT at Ser473. The expression level of the slit-diaphragm proteins Nephrin and TRPC6 as well as the cytoskeletal adaptor protein Nck significantly decreased. Moreover, Rapamycin reduced cell adhesion and cell motility, which was accompanied by an enhanced formation of dot-like Actin rich structures. Our data provide new molecular insights, explaining which pathways and molecules are affected in podocytes by an imbalanced mTOR function due to Rapamycin treatment.