The operant conditioning has been less studied than the classical conditioning as a mechanism of placebo-like effect, and two distinct learning mechanisms have never been compared to each other in terms of their neural activities. Twenty-one participants completed cue-learning based pain rating tasks while their brain responses were measured using functional magnetic resonance imaging. After choosing (instrumental) or viewing (classical) one of three predictive cues (low- and high-pain cues with different level of certainty), they received painful stimuli according to the selected cues. Participants completed the same task during the test session, except that they received only a high pain stimulus regardless of the selected cues to identify the effects of two learning paradigms. While receiving a high pain stimulation, low-pain cue significantly reduced pain ratings compared to high-pain cue, and the overall ratings were significantly lower under operant than under classical conditioning. Operant behavior activated the temporoparietal junction significantly more than the passive behavior did, and neural activity in the primary somatosensory cortex was significantly reduced during pain in instrumental as compared with classical conditioning trials. The results suggest that pain modulation can be induced by classical and operant conditioning, and mechanisms of attention and context change are involved in instrumental learning.