Acute pericoronitis (AP) is a common cause of odontogenic toothache. Pain significantly affects the structure and function of the brain, but alterations in spontaneous brain activity in patients with AP are unclear. To apply the amplitude of low-frequency fluctuations (ALFF) method in resting-state functional magnetic resonance imaging to investigate altered spontaneous brain activity characteristics in patients with AP in different frequency bands (typical, slow-4, and slow-5 bands) and assess their correlation with clinical scores. Thirty-four right-handed patients with AP and 31 healthy controls (HC), matched for age, sex, education, and right-handedness, were enrolled. All subjects underwent resting-state functional magnetic resonance imaging. DPABI software was used for data preprocessing and extracting the ALFF values in different frequency bands. Subsequently, differences in ALFF values in the three bands were compared between the two groups. Correlation between ALFF values in the differential brain regions and clinical scores was assessed. In the typical band, ALFF values were higher in the left insula, left superior occipital gyrus, left inferior parietal lobule, left posterior cerebellar lobule, and right postcentral gyrus in the AP than in the HC group. In the slow-4 band, ALFF values in the left superior occipital gyrus, right superior occipital gyrus, and right middle occipital gyrus were higher, and those in the right cingulate gyrus and right superior temporal gyrus were lower in the AP than in the HC group. In the slow-5 band, the ALFF values in the left insula and left superior occipital gyrus were higher in the AP than in the HC group. The ALFF values of the typical bands in the left insula, left inferior parietal lobule, and right postcentral gyrus correlated negatively, those of the slow-4 band in the right middle occipital gyrus correlated positively, and those of the slow-5 band in the left insula correlated negatively with the visual analogue scale score in the AP group. Our results suggested that the intrinsic brain activity of AP patients was abnormal and frequency-dependent. This provides new insights to explore the neurophysiological mechanisms of AP.