In the future, the cultivation of maize will become more and more prominent. As the world’s demand for food and animal feeding increases, remote sensing technologies (RS technologies), especially unmanned aerial vehicles (UAVs), are developing more and more, and the usability of the cameras (Multispectral-MS) installed on them is increasing, especially for plant disease detection and severity observations. In the present research, two different maize hybrids, P9025 and sweet corn Dessert R78 (CS hybrid), were employed. Four different treatments were performed with three different doses (low, medium, and high dosage) of infection with corn smut fungus (Ustilago maydis [DC] Corda). The fields were monitored two times after the inoculation—20 DAI (days after inoculation) and 27 DAI. The orthomosaics were created in WebODM 2.5.2 software and the study included five vegetation indices (NDVI [Normalized Difference Vegetation Index], GNDVI [Green Normalized Difference Vegetation Index], NDRE [Normalized Difference Red Edge], LCI [Leaf Chlorophyll Index] and ENDVI [Enhanced Normalized Difference Vegetation Index]) with further analysis in QGIS. The gathered data were analyzed using R-based Jamovi 2.6.13 software with different statistical methods. In the case of the sweet maize hybrid, we obtained promising results, as follows: the NDVI values of CS 0 were significantly higher than the high-dosed infection CS 10.000 with a mean difference of 0.05422 *** and a p value of 4.43 × 10−5 value, suggesting differences in all of the levels of infection. Furthermore, we investigated the correlations of the vegetation indices (VI) for the Dessert R78, where NDVI and GNDVI showed high correlations. NDVI had a strong correlation with GNDVI (r = 0.83), a medium correlation with LCI (r = 0.56) and a weak correlation with NDRE (r = 0.419). There was also a strong correlation between LCI and GNDVI, with r = 0.836. NDRE and GNDVI indices had the correlation coefficients with a CCoeff. of r = 0.716. For hybrid separation analyses, useful results were obtained for NDVI and ENDVI as well.