Circulating tumor cells (CTCs) with different epithelial and mesenchymal phenotypes play distinct roles in the metastatic cascade. However, the influence of their phenotypic traits and chemotherapy on their transit and retention within capillaries remains unclear. To explore this, we developed a microfluidic device comprising 216 microchannels of different widths from 5 to 16 m to mimic capillaries. This platform allowed us to study the behaviors of human breast cancer epithelial MCF-7 and mesenchymal MDA-MB-231 cells through microchannels under chemotherapy-induced stress. Our results revealed that when the cell diameter to microchannel width ratio exceeded 1.2, MCF-7 cells exhibited higher transit percentages than MDA-MB-231 cells under a flow rate of 0.13 mm/s. Tamoxifen (250 nM) reduced the transit percentage of MCF-7 cells, whereas 100 nM paclitaxel decreased transit percentages for both cell types. These differential responses were partially due to altered cell stiffness following drug treatments. When cells were entrapped at microchannel entrances, tamoxifen, paclitaxel, and high-flow stress (0.5 mm/s) induced a reduction in mitochondrial membrane potential (MMP) in MCF-7 cells. Tamoxifen treatment also elevated reactive oxygen species (ROS) levels in MCF-7 cells. Conversely, MMP and ROS levels in entrapped MDA-MB-231 cells remained unaffected. Consequently, the viability and proliferation of entrapped MCF-7 cells declined under these chemical and physical stress conditions. Our findings emphasize that phenotypically distinct CTCs may undergo selective filtration and exhibit varied responses to chemotherapy in capillaries, thereby impacting cancer metastasis outcomes. This highlights the importance of considering both cell phenotype and drug response to improve treatment strategies.