Pain-related movement fear is a contributing factor to residual pain and functional deficits in chronic ankle instability (CAI), but its underlying neural mechanisms remain unclear. We aimed to (1) delineate whether participants with CAI exhibit discernible differences in specific emotion and pain-related brain regions, compared to a healthy control (HC) cohort and (2) explore potential neural mechanisms underlying pain and fear in participants with CAI, with an emphasis on investigating possible associations with pain-related neural plasticity. Cross-sectional study. University research laboratory. 28 participants with CAI (17males and 11 females; age: 31.28±6.31 years) and 28 HCs (16 males and 12 females; age: 30.18±7.59 years). We analyzed T1 structural imaging data from participants and assessed their fear of movement and pain intensity using the Tampa Scale for Kinesiophobia (TSK) and the Visual Analog Scale (VAS) for pain, respectively. We compared the mean gray matter (GM) density of pain-related area between the two groups and their correlations with the TSK and VAS scores. In comparison with the HC group, participants with CAI showed a significant decrease in the mean GM density in the prefrontal cortex (Cohen's d = -0.808) and periaqueductal gray (Cohen's d = -0.934). In participants with CAI, the mean GM density of the prefrontal cortex (PFC) was negatively correlated with the TSK scores (r = -0.531). During intense exercise, the mean GM density of the periaqueductal gray (PAG) was negatively correlated with the VAS scores (r = -0.484). Additionally, TSK scores were positively correlated with VAS scores (r = 0.455). Our exploratory findings suggest that, in participants with CAI, the atrophy of the PFC and PAG may be associated with pain-related fear. Future clinical diagnosis and treatment for CAI should consider the impact of psychological barriers on functional recovery.