The accumulation of antibiotics by plants is a currently concern associated to yield reduction and transference of antibiotic residues along the food web. Maize is a staple food in many parts of the world; it is also considered an important ingredient in animal nutrition. Considering the lack of validated analytical methods for the analysis of ciprofloxacin (CIPRO) and enrofloxacin (ENRO) in the shoot of Zea mays maize, we developed a reliable reversed-phase high-performance liquid chromatography method with fluorescence detection (HPLC-FLD). This method was validated for linearity, matrix effects, precision, accuracy, limits of quantification (LOQ) and detection (LOD), and robustness. The analytical curves were linear with coefficient of determination (R2) of 0.9907 for CIPRO and 0.9962 for ENRO. The LOD values were 16.65 and 6.57 μg kg−1 for CIPRO and ENRO, respectively, whereas LOQ values were 50.44 μg kg−1 (CIPRO) and 19.92 μg kg−1 (ENRO). HPLC-FLD also displayed good precision and accuracy. Therefore, the proposed method can be considered a reliable and useful tool for the analysis of ciprofloxacin and enrofloxacin in the shoot of maize.