The purpose of this study was to evaluate the effects of hyperbaric oxygen therapy (HBOT) on reducing neurological sequelae (NS) in patients with carbon monoxide poisoning (COP). Using a nationwide database of insurance claims in Taiwan, we conducted a population-based cohort study to identify 24,046 patients with COP diagnosed between 1999 and 2012, including 6793 (28.2%) patients who received HBOT and 17,253 (71.8%) patients who did not. We followed the two cohorts of patients and compared the occurrence of NS. The two cohorts had similar sex ratios, but patients who received HBOT were younger (34.8 ± 14.8 vs. 36.1 ± 17.2 years, p < 0.001). Patients who received HBOT had a higher risk for NS (adjusted hazard ratio [AHR]: 1.4; 95% confidence interval [CI]: 1.4–1.5), after adjusting for age, sex, underlying comorbidities (hypertension, diabetes, chronic obstructive pulmonary disease, hyperlipidemia, malignancy, coronary artery disease, congestive heart failure, liver disease, renal disease, connective tissue disease, human immunodeficiency virus [HIV] infection, and alcoholism), monthly income, suicide, drug poisoning, and acute respiratory failure. We observed similar findings when we stratified the patients by age, sex, underlying comorbidities, and monthly income. The increased risk was most prominent in the first 2 weeks (AHR: 2.4; 95% CI: 2.1–2.7) and remained significant up to 6 months later (AHR: 1.6; 95% CI: 1.4–1.7). The risk for NS was higher in patients with COP who received HBOT than in those who did not, even after considering the possible impact of longer observation periods on survivors. Further studies that included the potential confounding factors we did not measure are needed to confirm findings in this study.