In this study, we present a polymer optical fiber fluorophore/aptamer competitive assay-based cortisol sensing principle. We developed a low-cost, two-fiber perpendicular design for fluorophore-based sensing with less input light interference and high output signal intensity. The design is suitable for narrow stokes shift fluorophores. We have demonstrated the cortisol sensing principle based on the competition between tagged and normal cortisol. To date, the sensing design has exhibited a slow response, and we identified possible modifications for improvement. Our estimation shows that with miniaturization and a modified sensor assay compartment design, a less than one-hour response time can be achieved. The reported sensing principle and low-cost new design will be helpful for the future development of fluorophore-based fiber optic aptasensors that can potentially be used in a wet environment for online sensing.