Timely and accurate estimates of sugarcane yield provide valuable information for food management, bio-energy production, (inter)national trade, industry planning and government policy. Remote sensing and machine learning approaches can improve sugarcane yield estimation. Previous attempts have however often suffered from too few training samples due to the fact that field data collection is expensive and time-consuming. Our study demonstrates that unmanned aerial vehicle (UAV) data can be used to generate field-level yield data using only a limited number of field measurements. Plant height obtained from RGB UAV-images was used to train a model to derive intra-field yield maps based on 41 field sample plots spread over 20 sugarcane fields in the Udon Thani Province, Thailand. The yield maps were subsequently used as reference data to train another model to estimate yield from multi-spectral Sentinel-2 (S2) imagery. The integrated UAV yield and S2 data was found efficient with RMSE of 6.88 t/ha (per 10 m × 10 m pixel), for average yields of about 58 t/ha. The expansion of the sugarcane yield mapping across the entire region of 11,730 km2 was in line with the official statistical yield data and highlighted the high spatial variability of yields, both between and within fields. The presented method is a cost-effective and high-quality yield mapping approach which provides useful information for sustainable sugarcane yield management and decision-making.