Rust, putatively caused by Puccinia emaculata, is a widespread and potentially damaging disease of switchgrass, a crop produced as feedstock for livestock and bioenergy. Azoxystrobin, chlorothalonil, and myclobutanil were applied at 1-, 2-, 3-, or 4-wk intervals for 12 to 14 wks to the vegetatively propagated switchgrass cultivar ‘Cloud Nine’ to assess fungicide selection and application interval for the control of rust as well as the impact of this disease on switchgrass biomass yield. While rust severity significantly differed among study years, azoxystrobin and myclobutanil were often equally and more effective than chlorothalonil at controlling rust, with superior disease control coming at the shorter compared to extended application intervals. Year, product, application interval, and product × interval significantly impacted dry biomass yield, which was greatest in 2016 and lowest in 2014. Dry biomass yield protection was significantly better with azoxystrobin and myclobutanil applications than with chlorothalonil or no fungicide. Linear regression models with the final disease rating, as well as with AUDPC in each year, were significant but coefficients of determination were low to moderate (0.21 < R2 < 0.60), indicating that rust response and subsequent disease impact on dry biomass yield were impacted by other factors. From our models, an estimated 3 to 5% biomass decline was calculated for each 10% increment in rust-related leaf necrosis observed at the final September rating date. With rust-related leaf necrosis > 80% by 1 Sept in each of four study years, biomass yield may be reduced by 24 to 40% if rust problems are not managed in switchgrass crops.