Biological repellents have been used as a control method to mitigate human-wildlife conflict worldwide. We aimed to evaluate the effect of jaguar (Panthera onca) feces as a repellent for a free-living urban population of capybaras (Hydrochoerus hydrochaeris), which are considered a vertebrate pest in some regions of their range. Observational data were collected during two consecutive 5-day periods: control and treatment. Scan samples within a 2-h observational session were carried out, recording capybara incursions into a 15 m × 15 m marked perimeter and alertness behavioral state. During the treatment period, 30 g of jaguar feces were added daily every 5.0 m around the perimeter in four selected areas (around Lake Paranoa, Brasilia, Brazil) frequented by capybara. The presence of predator feces induced changes in capybaras’ behavior as there was a decrease in actual presence at the sites as a whole with the presence of jaguar feces. Of those capybaras that did continue to visit a site, incursions into the marked perimeter were initially greatly reduced, but did rebound relatively rapidly over the trial period. Although our results showed that capybaras recognize jaguar’s feces as a predator threat, odor habituation may limit the repellent’s efficacy at a local level, but appeared to have a longer term effect on the overall numbers of capybara visiting a site in general. Improvements in this technique will be required for it to become practicable, to reinforce capybaras’ aversion to predators, to decrease their habituation to predator’s feces, and to provide more humanitarian control.