We compared the activation pattern at the motor cortex (MC and prefrontal cortex (PFC) based on the delta value (Δ) of oxy-hemoglobin (HbO) by functional near-infrared spectroscopy (fNIRS). We examined the relationship of the ΔHbO based on the peaks at 5°C and 25°C by right-hand immersion in water in 22 fibromyalgia and 19 controls. Fibromyalgia showed a shorter peak latency for HbO at the left MC. In contrast, at the left MC, their HbO increased 117.64% compared to 92.85% in the controls. A receiver operator characteristics (ROC) analysis showed the ΔHbO cutoffs equal to –0.175 at the left and –0.205 at the right PFC offer sensitivity and specificity of at least 80% in screening fibromyalgia compared to controls. In fibromyalgia, a ROC analysis showed that these cutoff points could discriminate those with higher disability due to pain and more severe central sensitization symptoms (CSS). The ROC with the best discriminatory profile was to the CSS score with the ΔHbO at the left PFC (AUC = 0.82, CI 95% = 0.61–100). These results indicate that cortical activation based on the ΔHbO at the PFC might be a sensitive marker to identify those fibromyalgia patients with more severe clinical symptoms.