To determine whether the neutrophil-to-high-density lipoprotein cholesterol ratio (NHR) can predict the functional outcome of a first-episode acute ischemic stroke (AIS) after 90 days, a retrospective cohort study was carried out. Consecutive AIS patients admitted to Suining Central Hospital within 72 hours of symptom onset between August 2022 and August 2023 were screened, and 527 patients with complete clinical, laboratory, imaging and follow-up data were included. Functional outcome was assessed at 90 days after the modified Rankin Scale, and scores of 0-2 were considered a favourable outcome; scores of 3-6 were considered a poor outcome. NHR was calculated based on the admission neutrophil count and HDL-C, and then its prognostic value was investigated through quartile grouping, binary logistic regression, receiver operating characteristic (ROC) curve analysis and pre-specified subgroup analysis. A poor outcome occurred in 199 cases (37.8%). The optimal NHR cutoff was 4.724, and continuous NHR was still independently associated with poor 90-day outcomes after adjusting for age, sex, admission NIHSS score, stroke type, atrial fibrillation, coronary heart disease, neutrophil count, lymphocyte count and HDL-C (OR 2.19, 95% CI 1.50-3.18, p < 0.001). NHR achieved an AUC of 0.716 and was relatively high among the other composite inflammatory indices and close to NLR. Subgroup analysis showed a stronger association among males, patients older than 70 years, hypertensive patients, non-diabetic patients, and those with moderate- to severe baseline neurological deficits. Based on the above studies, NHR can be used as a relatively easy-to-obtain marker for short-term risk assessment after an AIS, but multi-center verification and mechanistic investigations are still needed.