Uncertainty has been demonstrated to influence the perception of noxious stimuli, but little is known about the effects of prolonged uncertain contexts on the perception of painful and non-painful stimuli. To address this knowledge gap, the present study utilized a cue-based NPU-threat task, where uncertain and certain trials were separated into distinct blocks. The objective was to investigate the impact of uncertain contexts on the temporal dynamics of electroencephalogram (EEG) activity during the processing of painful and non-painful stimuli. The results revealed that the influence of uncertain contexts on neural responses extends beyond painful trials and is also evident in non-painful trials. In uncertain contexts, it has been observed that painful stimuli elicit larger P2 amplitudes and late beta band (13-30 Hz) event-related desynchronization (ERD) around 500-700 ms. However, in certain contexts, painful stimuli evoke stronger late gamma band (50-70 Hz) event-related synchronization (ERS) around 600-700 ms. For non-painful trials, in uncertain contexts, significantly higher amplitudes of the late positive potential (LPP) component and delta-theta band (2-7 Hz) ERS were observed compared to certain non-painful stimuli. These findings demonstrate that uncertain contexts exert a significant impact on the processing of both painful and non-painful stimuli, and this influence is mediated by distinct neural mechanisms.