Background: Heart rate (HR) and respiratory rate (RR) can be challenging to measure accurately and reliably in neonates. The introduction of innovative, non-invasive measurement technologies suitable for resource-constrained settings is limited by the lack of appropriate clinical thresholds for accuracy comparison studies. Methods: We collected measurements of photoplethysmography-recorded HR and capnography-recorded exhaled carbon dioxide across multiple 60-second epochs (observations) in enrolled neonates admitted to the neonatal care unit at Aga Khan University Hospital in Nairobi, Kenya. Trained study nurses manually recorded HR, and the study team manually counted individual breaths from capnograms. For comparison, HR and RR also were measured using an automated signal detection algorithm. Clinical measurements were analyzed for repeatability. Results: A total of 297 epochs across 35 neonates were recorded. Manual HR showed a bias of -2.4 (-1.8%) and a spread between the 95% limits of agreement (LOA) of 40.3 (29.6%) compared to the algorithm-derived median HR. Manual RR showed a bias of -3.2 (-6.6%) and a spread between the 95% LOA of 17.9 (37.3%) compared to the algorithm-derived median RR, and a bias of -0.5 (1.1%) and a spread between the 95% LOA of 4.4 (9.1%) compared to the algorithm-derived RR count. Manual HR and RR showed repeatability of 0.6 (interquartile range (IQR) 0.5-0.7), and 0.7 (IQR 0.5-0.8), respectively. Conclusions: Appropriate clinical thresholds should be selected a priori when performing accuracy comparisons for HR and RR. Automated measurement technologies typically use a smoothing or averaging filter, which significantly impacts accuracy. A wider spread between the LOA, as much as 30%, should be considered to account for the observed physiological nuances and within- and between-neonate variability and different averaging methods. Wider adoption of thresholds by data standards organizations and technology developers and manufacturers will increase the robustness of clinical comparison studies.