Portable health diagnostic systems seek to perform medical grade diagnostics in non-ideal environments. This work details a robust fault tolerant portable health diagnostic design implemented in hardware, firmware and software for the detectionof HPV in low-income countries. The device under device under test (DUT) is a fluorescence based lateral flow assay (LFA) point-of-care (POC) device. This work’s contributions are: firmware and software development, calibration routine implementation, device performance characterization and a proposed method of in-software fault detection. Firmware was refactored from the original implementation of the POC fluorescence reader to expose an application programming interface (API) via USB. Companion software available for desktop environments (Windows, Mac and Linux) was created to interface with this firmware API and conduct macro level routines to request and receive fluorescence data while presenting a user-friendly interface to clinical technicians. Lastly, an environmental chamber was constructed to conduct sequential diagnostic reads in order to observe sensor drift and other deviations that might present themselves in real-world usage. The results from these evaluations show a standard deviation of less than 1% in fluorescence readings in nominal temperature environments (approx. 25C) suggesting that this system will have a favorable signal-to-noise (SNR) ratio in such a setting. In non-ideal over heated environments (≥38C), the evaluation results showed performance degradation with standard deviations as large as 15%.