Recent advances in the development of microfluidic systems for the culture of complex and three-dimensional cell, tissue, and organ models allow their use in toxicity studies and mimicking many diseases. These types of in vitro models are important because of the huge advantages over standard two-dimensional cell cultures: better mimicking of in vivo conditions and more reliable response to the tested drugs. This report presents a new approach to modeling skin cancer (melanoma-on-a-chip) and breast cancer (breast cancer-on-a-chip) using the microfluidic systems. We designed a microfluidic device to co-culture cancer cells with non-malignant cells, which are the main component of the cancer microenvironment. In the construction of the microsystem, we used a scaffold in the form of a porous membrane made of poly(ethylene terephthalate), which enables the regular and reproducible arrangement of cells in the culture and maintains intercellular communication. To demonstrate the functionality of the microsystem, we used it to analyze the effectiveness of photodynamic therapy in the treatment of melanoma and chemotherapy in the treatment of breast cancer. The developed microsystem can be successfully used to model cancer diseases, especially with a layered arrangement of cells in the cancerous tissue, such as melanoma, ductal breast cancer, or breast cancer metastases to the skin.