AbstractAs anthropogenic impacts on ecosystems increase, novel solutions are needed to mitigate increasing human–wildlife conflict. Aversive conditioning is one strategy that can reduce the risks of humans living alongside wildlife by modifying the behavior of animals through their experiences with humans. Although considered rare, American alligator (Alligator mississippiensis) attacks on humans most often occur in human‐dominated landscapes and can be fatal. Our goal was to determine if capture and release protocols might serve as a form of aversive conditioning to reduce alligator tolerance of humans. Specifically, we compared the behavioral response of alligators in South Carolina, USA, in 2009–2018 to an approaching human for animals with 3 different levels of capture experience: alligators from a reference site where no captures occurred, alligators from a site where captures occurred that directly experienced capture and release, and alligators from the site where captures occurred that indirectly experienced capture and release (never captured but likely observed capture of others). We used a hurdle model and information‐theoretic approach to evaluate support for 8 hypotheses regarding factors that influence alligator probability of flight in response to an approaching human and the flight initiation distance (FID) of alligators that did flee. Our hypotheses considered the effects of capture experience, exposure to non‐capture (visual) surveys, alligator size, ambient temperature, and season. The best‐supported models provided strong evidence that capture experience increased the probability of flight and, to a lesser extent, increased FID of alligators that did flee, but that the strength of the effect varied with alligator size or some correlate. Furthermore, the effect of capture may extend beyond animals with direct experience. Capture and release protocols can result in an aversive conditioning response in alligators, effectively reducing habituation to humans. Given the geographic limitations of our study, more work is necessary to determine whether the utility of aversive conditioning may be site‐dependent, or similarly effective across a wider selection of developed landscapes.