The varied effects of expectations on auditory perception are not well understood. For example, both top-down rules and bottom-up stimulus regularities generate expectations that can bias subsequent perceptual judgments. However, it is unknown whether these different sources of bias use the same or different computational and physiological mechanisms. We examined how rule-based and stimulus-based expectations influenced human subjects’ behavior and pupil-linked arousal, a marker of certain forms of expectation-based processing, during an auditory frequency-discrimination task. Rule-based cues biased choice and response times (RTs) toward the more-probable stimulus. In contrast, stimulus-based cues had a complex combination of effects, including choice and RT biases toward and away from the frequency of recently heard stimuli. These different behavioral patterns also had distinct computational signatures, including different modulations of key components of a novel form of a drift-diffusion model, and distinct physiological signatures, including substantial bias-dependent modulations of pupil size in response to rule-based but not stimulus-based cues. These results imply that different sources of expectations can modulate auditory perception via distinct mechanisms: one that uses arousal-linked, rule-based information and another that uses arousal-independent, stimulus-based information to bias the speed and accuracy of auditory perceptual decisions.