This work has been submitted to the IEEE Transactions on Biomedical Engineering for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible. Objective: Fetal heart rate (FHR) is critical for perinatal fetal monitoring. However, motions, contractions and other dynamics may substantially degrade the quality of acquired signals, hindering robust tracking of FHR. We aim to demonstrate how use of multiple sensors can help overcome these challenges, and improve measurement of desired signal. Methods: We develop KUBAI, a novel stochastic sensor fusion algorithm, to improve FHR monitoring accuracy. To demonstrate the efficacy of our approach, we evaluate it on data collected from gold standard large pregnant animal models, using a novel non-invasive fetal pulse oximeter. Results: The accuracy of the proposed method is evaluated against invasive ground-truth measurements. We obtained below 6 beats-per-minute (BPM) root-mean-square error (RMSE) with KUBAI, on five different more than 30-minutes long datasets. KUBAI’s performance is also compared against a single-sensor version of the algorithm to demonstrate the improvement in accuracy due to sensor fusion. KUBAI’s multi-sensor estimates are found to give 23.5% to 84% lower RMSE than single-sensor FHR estimates. Furthermore, KUBAI is shown to have 84% lower RMSE and ∼3 times higher R2 correlation with reference compared to another multi-sensor FHR tracking method found in literature. Conclusion: The results support the effectiveness of KUBAI, the proposed sensor fusion algorithm, to non-invasively and accurately estimate fetal heart rate with varying levels of noise in the measurements. Significance: The presented method can benefit other multi-sensor measurement setups, which may be challenged by low measurement frequency, low signal- to-noise ratio, or intermittent loss of signal in measurements.