Radiation use efficiency (RUE) is a parameter that is directly associated to yield, but difficult to estimate and unreasonable to estimate on a small plot research scale using traditional techniques. It has the potential to be used for evaluation of in-season management techniques and disease impact. During 2018 and 2019, field experiments located in north central and south western Iowa were used to investigate the estimation of RUE of soybean (Glycine max (L.) Merr.) and the effects of foliar fungicides across varying levels of frogeye leaf spot severity caused by the pathogen Cercospora sojina K. Hara. The objective of this research was to (i) demonstrate that it is possible to estimate RUE for soybean based on reflectance data derived from consumer-grade UAV imagery, (ii) determine how foliar fungicides affected frogeye leaf spot, remotely sensed plant health indicators, and soybean yield, and (iii) compare the impact of foliar fungicides and frogeye leaf spot on RUE estimated by using UAV reflectance data with a reduced sampling approach across foliar fungicide treatments. RUE of soybean was estimated by using UAVs to capture imagery on a high spatial and temporal scale. Values ranged from 0.98 to 1.07 and 0.96 to 1.12 across the entire season with 14 sampling dates and the period post-fungicide application with eight sampling dates, respectively. These values fall within the range of previously published soybean RUE values. The highest levels of frogeye leaf spot severity were recorded in Lewis 2018, and were just under 20%. At this location, the application of flutriafol + fluoxastrobin resulted in 19% more yield (P = 0.080) than the non-treated control. In addition, the frogeye leaf spot severity of the flutriafol + fluoxastrobin treatment was significantly (P = 0.010) less than the severity of the fluxapyroxad + pyraclostrobin treatment and non-treated control. Applications of foliar fungicides significantly (P = 0.012) increased canopy cover, but NDVI, SPAD, and RUE values did not differ between fungicide treatments. All RUE values estimated in Lewis 2018, Kanawha 2018, and Kanawha 2019 fell within the range of known values even with the reduced sampling approach. Pathogen specific impacts on soybean may confound the variables needed to estimate RUE. Using RUE to estimate the impact of disease on yield remotely may be a valuable resource; however, confounding factors will require additional work to use RUE within certain pathosystems.