Xylella fastidiosa subsp. pauca (Xfp) is one of the most dangerous plant pathogens in the world. Identified in 2013 in olive trees in south–eastern Italy, it is spreading to the Mediterranean countries. The bacterium is transmitted by insects that feed on sap, and causes rapid wilting in olive trees. The paper explores the use of Unmanned Aerial Vehicle (UAV) in combination with a multispectral radiometer for early detection of infection. The study was carried out in three olive groves in the Apulia region (Italy) and involved four drone flights from 2017 to 2019. To classify Xfp severity level in olive trees at an early stage, a combined method of geostatistics and discriminant analysis was implemented. The results of cross-validation for the non-parametric classification method were of overall accuracy = 0.69, mean error rate = 0.31, and for the early detection class of accuracy 0.77 and misclassification probability 0.23. The results are promising and encourage the application of UAV technology for the early detection of Xfp infection.