Fluorescence detection is one of the most widely used techniques for measuring analyte concentration in biological applications. Although used frequently with bulk systems, there are important considerations in using this approach in thin (<100μm) microfluidic lab-on-a-chip (LOC) systems in relating the measured fluorescence signal to analyte concentration. In this work, a general relationship between the photoresponse of an on-chip organic photodetector (OPD) and concentration of a fluorescent dye Rhodamine 6G in a microfluidic chip is presented. The developed theoretical model for photoresponse matches well to the extreme sub-linearity observed in measurements in a dilution series from 10nM to 1mM. The influence of the system factors, such as noise, detector sensitivity, and optical power were also analyzed to indicate design changes to improve the system performance and limits of detection even further.