Crop evapotranspiration (ET) is a crucial component of energy and water budgets. The accurate determination of ET is vital for agricultural water management. Several satellite-based ET models have been developed to map ET at the field to regional scales. The spatial resolution of the satellite observations, particularly thermal-infrared imagery, is insufficient to estimate ET for small (<1  ha) agricultural fields. With unmanned aerial vehicle (UAV) technology advancement, high spatial and temporal images can be acquired with UAVs to monitor ET for small fields or even at a canopy scale. The aim of this study was the evaluation of the two-source energy balance (TSEB) model to estimate daily and seasonal crop (bell pepper) ET (ET_TSEB) using high-resolution visible and thermal UAV imagery. Also, the impact of using different pixel resolutions (40, 50, 60, and 70 cm) with TSEB is compared with ET values derived using a soil water budget approach (ET_SWD) with a profile soil water content. The results of this study showed that there is a high correlation between ET_TSEB and ET_SWD values (R²  =  0.73 for daily, R²  =  0.98 for seasonal). The root mean square error values for daily and seasonal ET_TSEB are 0.62  mm day^−  1 and 11.46  mm season^−  1, respectively. The sensitivity of TSEB output to the spatial resolution indicated that different pixel resolutions do not significantly impact ET estimates. We suggest that the TSEB model has a real potential for agricultural water management applications for small agricultural fields using high-resolution UAV multispectral and thermal images.