In the context of precision agriculture (PA), geomatic surveys exploiting UAV (unmanned aerial vehicle) platforms allow the dimensional characterization of trees. This paper focuses on the use of low-cost UAV photogrammetry to estimate tree height, as part of a project for the phytoremediation of contaminated soils. Two study areas with different characteristics in terms of mean tree height (5 m; 0.7 m) are chosen to test the procedure even in a challenging context. Three campaigns are performed in an olive grove (Area 1) at different flying altitudes (30 m, 40 m, and 50 m), and one UAV flight is available for Area 2 (42 m of altitude), where three species are present: oleander, lentisk, and poplar. The workflow involves the elaboration of the UAV point clouds through the SfM (structure from motion) approach, digital surface models (DSMs), vegetation filtering, and a GIS-based analysis to obtain canopy height models (CHMs) for height extraction based on a local maxima approach. UAV-derived heights are compared with in-field measurements, and promising results are obtained for Area 1, confirming the applicability of the procedure for tree height extraction, while the application in Area 2 (shorter tree seedlings) is more problematic.