There is a growing concern about water scarcity and the associated decline in Australia’s agricultural production. Efficient water use as a natural resource requires more precise and adequate monitoring of crop water use and irrigation scheduling. Therefore, accurate estimations of evapotranspiration (ET) at proper spatial–temporal scales are critical to understand the crop water demand and uptake and to enable optimal irrigation scheduling. Remote sensing (RS)-based ET estimation has been adopted as a method for large-scale applications when the detailed spatial representation of ET is required. This research aimed to estimate instantaneous ET using very-high-resolution (VHR) multispectral and thermal imagery (GSD < 8 cm) collected using a single flight of a UAV over a high-density peach orchard with a discontinuous canopy. The energy balance component estimation was based on the high-resolution mapping of evapotranspiration (HRMET) model. A tree-by-tree ET map was produced using the canopy surface temperature and the leaf area index (LAI) resampled at the corresponding scale via a systematic feature segmentation method based on pure canopy extraction. Results showed a strong linear relationship between the estimated ET and the leaf transpiration (n = 42) measured using a gas exchange sensor, with a coefficient of determination (R2) of 0.89. Daily ET (5.5 mm d−1) derived from the instantaneous ET map was comparable with daily crop ET (6.4 mm d−1) determined by the meteorological approach over the study site. The proposed approach has important implications for mapping tree-by-tree ET over horticultural fields using VHR imagery.