The research aimed to evaluate the spectral behavior of remotely piloted aircraft system (RPAS) images taken of agricultural crops during the day to answer the following hypotheses: (1) there are no significant differences between spectral reflectance information obtained through RPAS images and data from spectroradiometry; (2) the survey time can be defined as a limiting factor in obtaining accurate reflectance data; and (3) it is possible to characterize homogeneous observation windows throughout the day. With regular intervals of 1 h, 12 surveys were made in rice and soybean cultivars, using a Sequoia^® camera, embedded in RPAS, and the FieldSpec^®3 spectroradiometer, to validate the image spectra. Normalized Difference Vegetation Index (NDVI), Optimized Soil Adjusted Vegetation Index (OSAVI), and Transformed Chlorophyll Absorption Reflectance Index (TCARI) derived from aerial images were subjected to Kruskal–Wallis and hierarchical cluster tests to define homogeneous observation times. The Sequoia^® system made it possible to obtain reflectance data that met the validation criteria, even operating under varying interaction factors during the day, so the flight schedule did not result in loss of information about the vegetation. The hierarchical cluster analysis allowed the detection of temporal patterns of NDVI, OSAVI, and TCARI throughout the day. For rice and soybeans, three more homogeneous observation windows were characterized. In terms of temporal pattern of NDVI, OSAVI, and TCARI, the Kruskal–Wallis analysis was quite sensitive to the inherent variation of the crops throughout the day, so a hypothesis of homogeneous monitoring windows input throughout the day could not be proven.