Background: Fragile X syndrome (FXS) is a genetic condition associated with increased risk for social anxiety and avoidance. Using functional near-infrared spectroscopy (fNIRS), we previously demonstrated aberrant neural activity responding to faces in young girls with FXS cross-sectionally. Here, we tested the hypothesis that abnormalities in neural activation and sensitization would increase with age in 65 girls with FXS (ages 6–16 years) relative to an age-matched control group of 52 girls who had comparable cognitive function and clinical symptoms. Methods: fNIRS data were collected at 2 time points (mean [SD] = 2.8 [0.6] years apart) during a face processing task. Linear mixed-effect models examined longitudinal neural profiles in girls with FXS and control participants. Correlational analysis was performed to examine associations between neural sensitization (increasing neural response to repeated stimuli) and clinical ratings. Results: In the FXS group, 24 participants had 1 fNIRS scan, and 32 had 2 scans. In the control group, 28 participants had 1 fNIRS scan, and 22 had 2 scans. Brain activations in the superior frontal gyrus were higher in girls with FXS than control participants at both time points. Neural sensitization also increased in girls with FXS at a higher rate than control participants in the superior frontal gyrus when responding to upright faces. For the FXS group, sensitization in the superior frontal gyrus positively correlated with longitudinal increases in anxiety and social avoidance scores. Conclusions: Girls with FXS show increasingly abnormal neural activation and sensitization responding to faces over time. Aberrant neural sensitization in girls with FXS is associated with longitudinal changes in anxiety and social skills.