Conventional cell-based assays in life science and medical applications can be difficult to maintain functionally over long periods. Microfluidics is an emerging technology with potential to provide integrated environments for cell maintenance, continuous perfusion, and monitoring. In this study, we developed an integrated microfluidic device with on-chip pumping and detection functionalities. The microfluidic structure in the device is divided into two independent channels separated by a semipermeable membrane on which cells are inoculated and cultured. Perfusion and fluorescence measurements of culture media for each channel can be conducted by the on-chip pumping system and optical fiber detection system. Performance of the device was examined through long-term culture and monitoring of polarized transport activity of intestinal tissue models (Caco-2 cells). The cells could be cultured for more than two weeks, and monolayer transport of rhodamine 123 was successfully monitored by on-line fluorescent measurement. This device may have applications in toxicity testing and drug screening.