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Background: Retinal dystrophies related to damaging variants in the cadherin-related family member 1 (<i>CDHR1</i>) gene are rare and phenotypically heterogeneous. Here, we report a longitudinal (three-year) structure–function evaluation of a patient with a <i>CDHR1</i>-related retinal dystrophy. Methods: A 14-year-old girl was evaluated between 2019 and 2022. An ophthalmological assessment, including color vision, perimetry, electroretinography, and multimodal imaging of the retina, was performed periodically every six months. Next-generation sequencing disclosed two likely pathogenic/pathogenic variants in the <i>CDHR1</i> gene, in compound heterozygosity, confirmed by segregation analysis. Results: At first examination, the patient showed a cone–rod pattern retinal dystrophy. Over follow-up, there was a decline of visual acuity and perimetric sensitivity (by ≥0.3 and 0.6 log units, respectively). Visual loss was associated with a progressive increase in inner retinal thickness (by 30%). Outer retina showed no detectable changes over the follow-up. Conclusions: The results indicate that, in this patient with a <i>CDHR1</i>-related cone–rod dystrophy, the progression to severe visual loss was paralleled by a progressive inner retinal thickening, likely a reflection of remodeling. Inner retinal changes over time may be functionally relevant in view of the therapeutic attempts based on gene therapy or stem cells to mitigate photoreceptor loss.