In the context of precision agriculture (PA), geomatic surveys exploiting UAV platforms allow the trees’ dimensional characterization and crown identification. This paper focuses on the use of low-cost UAV photogrammetry to estimate the trees’ height, as part of a project for the phytoremediation of contaminated soils. Two study areas (Area 1; Area 2) have been chosen, having different characteristics in terms of mean trees’ height (5 m; 0.7 m), to test the procedure even in a challenging context. Three campaigns have been performed in Area 1 at different altitudes (30 m, 40 m, 50 m), and one UAV flight is available in Area 2 (42 m of altitude). The implemented workflow involves the elaboration of the UAV point clouds and DSMs using the standard SfM approach, the vegetation filtering, the generation of the DTM and a GIS-based analysis to obtain the CHMs for the extraction of the trees’ heights based on a local maxima approach. UAV-derived heights have been compared with in-field measurements obtaining promising results in Area 1, confirming the applicability of the procedure for trees’ height extraction, while the application in the context of low trees was more problematic.