Unbound cortisol in saliva, which can be detected with non-invasive sampling, is now considered as one of the most effective biomarkers for the biochemical evaluation of common mental disorders. In this work, a new polymer lab-on-a-chip (LOC) based on a microfluidic capillary flow assay (MCFA) with on-chip dried reagents was newly developed and fully characterized for the detection of unbound cortisol in saliva. The new MCFA device consisted of serially connected microchannels for sample loading, dried detection antibodies, time delay for incubation time control, a spiral reaction chamber for testing, positive and negative controls, and a capillary pump for waste fluid collection. In addition, a portable fluorescence analyzer was also developed for the rapid quantitative measurement of salivary cortisol with high accuracy. A linear dynamic range of 7.0 pg mL⁻¹–16.0 ng mL⁻¹ was achieved from spiked artificial saliva samples with an inter-chip CV of around 4.0% using the developed LOC and fluorescence analyzer. The achieved results support the effective biochemical analysis of common mental disorders such as chronic stress, depression, anxiety and post traumatic stress disorder (PTSD). The new LOC based on a microfluidic capillary flow assay (MCFA) developed in this work can be one of the most promising LOC platforms for high-sensitivity and quantitative POCT with saliva and blood plasma/serum samples.