In this study, a simple and rapid methodology to analyze and quantify principal flavanones in citrus fruit juices through the use of a nano-LC/UV-Vis apparatus, employing a 75 μm id capillary column packed with sub-2 μm particles C18 stationary phase for 10 cm, was developed. All compounds were baseline resolved working with a step gradient elution mode in 10 min. The developed analytical method was validated and the resulting RSD% for intra- and interday repeatability, related to retention time and peak area, were <4.7 and 5.5%, respectively. LOD and LOQ values corresponded to 0.40 and 1.56 μg/mL for didymin, hesperitin, and narinegenin, while for the other flavanones were 0.78 and 3 μg/mL, respectively. Good linearity with acceptable determination coefficients R(2) was obtained in the range between LOQ concentration and 200 μg/mL (500 μg/mL naringin and hesperidin). Good recovery values were also obtained. Then, the method was applied to the analysis of selected hand-squeezed and commercial citrus juices. Further, the nano-LC system was coupled to a mass spectrometer to confirm analyte identification. Antioxidant capacity of selected samples was also evaluated measured by Folin-Ciocalteu assay and Trolox equivalent antioxidant capacity assay. Results were compared to determine total flavanones concentrations.