This study presented a method to estimate areal mean rainfall (AMR) using a Biased Sentinel Hospital Based Area Disease Estimation (B-SHADE) model, together with biased rain gauge observations and Tropical Rainfall Measuring Mission (TRMM) data, for remote areas with a sparse and uneven distribution of rain gauges. Based on the B-SHADE model, the best linear unbiased estimation of AMR could be obtained. A case study was conducted for the Three-River Headwaters region in the Tibetan Plateau of China, and its performance was compared with traditional methods. The results indicated that B-SHADE obtained the least estimation biases, with a mean error and root mean square error of −0.63 and 3.48 mm, respectively. For the traditional methods including arithmetic average, Thiessen polygon, and ordinary kriging, the mean errors were 7.11, −1.43, and 2.89 mm, which were up to 1027.1%, 127.0%, and 358.3%, respectively, greater than for the B-SHADE model. The root mean square errors were 10.31, 4.02, and 6.27 mm, which were up to 196.1%, 15.5%, and 80.0%, respectively, higher than for the B-SHADE model. The proposed technique can be used to extend the AMR record to the presatellite observation period, when only the gauge data are available.