Applications involving fluorescence detection in point-of-care systems are both interesting and challenging in nature. The applications usually require a simple, compact, robust, highly sensitive yet affordable system. As a result, the system needs to be efficient in fluorescence detection by using practical and easily fabricated, hence inexpensive sensors. In this paper, a fluorescence sensor using an in-fiber microchannel has been developed and tested successfully. A blue LED, multimode PMMA or silica fiber, mini-PMT and fluorescein in PBS pH 7.4 buffer solution were used as the excitation source, light guide, fluorescence detector and sample, respectively. Microfluidic channels of 100μm width and 1cm length were fabricated in the optical fibers using a direct write CO2 laser system. The channels in the fibers were examined using a SEM and an optical microscope. Experimental results show that the sensor is highly sensitive, being able to detect 0.1 μg/L of fluorescein in the PBS buffer solution, with good signal to noise ratio and the results are reproducible. The data obtained using silica fibers as sensors when compared with the results from PMMA fibers show that the silica fiber sensor has better sensitivity than the PMMA fiber sensor. This could be due to the fouling effect created by the frosty layer at the bottom of the microchannel made within the PMMA fiber. Our future work will integrate the fiber sensor into microfluidic chips for lab-on-a-chip applications.