In 51 lesions from 15 patients with the inflammatory skin condition chronic graft‐versus‐host‐disease, hyperspectral imaging accurately delineated active erythema and post‐inflammatory hyperpigmentation. The method was validated by dermatologist‐approved confident delineations of only definitely affected and definitely unaffected areas in photographs. A prototype hyperspectral imaging system acquired a 2.5 × 3.5 cm2 area of skin at 120 wavelengths in the 450–850 nm range. Unsupervised extraction of unknown absorbers by endmember analysis achieved a comparable accuracy to that of supervised extraction of known absorbers (melanin, hemoglobin) by chromophore mapping: 0.78 (IQR: 0.39–0.85) vs. 0.83 (0.53–0.91) to delineate erythema and 0.74 (0.57–0.87) vs. 0.73 (0.52–0.84) to delineate hyperpigmentation. Both algorithms achieved higher specificity than sensitivity. Whereas a trained human confidently marked a median of 7% of image pixels, unsupervised and supervised algorithms delineated a median of 14% and 27% pixels. Hyperspectral imaging could overcome a fundamental practice gap of distinguishing active from inactive manifestations of inflammatory skin disease.