Melanoma is one of the most invasive skin cancers with the highest mortality risk. The PI3K/AKT/mTOR signaling pathways are a key regulatory point related to growth factors and involved in the cell's energy metabolism. They are responsible for cell life processes such as growth, proliferation, invasion, survival, apoptosis, autophagy, and angiogenesis. The studies undertaken concerned the effect of protein kinase inhibitors involved in the signaling pathways of AKT, MEK, and mTOR kinases on the expression of cytoskeletal and extracellular matrix proteins, invasion process, and activities of the matrix metalloproteinases (MMPs): MMP-2 and MMP-9 in melanoma cells. The study used mTOR kinase inhibitors: Everolimus and Torkinib; dual PI3K/mTOR inhibitors BEZ-235 and Omipalisib; and the mTORC1/2 inhibitor OSI-027. These compounds were used both as monotherapy and in combination with the MEK1/2 inhibitor AS-703026. mTOR kinase inhibitors, especially the third generation in combination with the MEK 1/2 kinase inhibitor AS-703026, significantly inhibited invasion and metalloproteinases (MMPs) activity in melanoma cell lines. The inhibition of the cell invasion process was accompanied by a significant change in the expression of proteins associated with EMT. The morphology of cells also changed significantly: their thickness, volume, roughness, convexity of shape, and irregularity, which may be a good diagnostic and prognostic factor for the response to treatment. Our studies to date on the effect of three generations of mTOR kinase inhibitors on the inhibition of the invasion process, the activation of apoptosis, and the reduction in cell proliferation suggest that they may be an important target for anticancer therapy.