We propose a sensor that provides position measurement for a particle in a micro channel fabricated with polydimethylsiloxane (PDMS) chip. By irradiating a plastic optical fiber (POF) array arranged across the micro channel with a light source, the particle position is measured by the change in POF output power. The effects of the optical axis misalignment between POF, the particle size and transmission were calculated to evaluate the measurement principle. We fabricated a sensor integrated with a PDMS micro channel made by soft lithography. The sensor was examined experimentally by measuring the output voltage from a photodiode and calculating the decrease in POF output power in the presence of a particle. The measurement result of our fabricated senor was compared with the particle image recorded with a CCD camera attached to a microscope. The experimental results indicate that our proposed sensor can be adapted for use in automated cell manipulation.