Background Lung infection may cause many symptoms, such as fever and headache, that may be confused with cryptococcal meningitis (CM) symptoms. This study aimed to investigate the discrepancy in clinical features and outcomes of CM between HIV-negative patients with and without lung infection.Methods We retrospectively reviewed the medical records of patients with CM admitted to two hospitals in Southwest China from 1 January 2014 to 31 December 2018.Results A total of 71 patients was included during the 5 years, among which 35 (49.3%) patients had lung disease. CM occurred more frequently in male (62.9% vs. 44.4%, P=0.12) and young (≤30 years, 31.4% vs. 16.7%, P=0.30) patients with lung infection than in the patients without lung infection, with more fever (77.1% vs. 30.6%, P=0.001) and less central nervous system symptoms (5.7% vs. 16.7%, P=0.28) and vomiting (25.0% vs. 14.3%, P=0.26). In addition, patients with lung infection presented higher percentages of white blood cell (WBC) counts ˂20×106/L (45.7% vs. 22.2%, P=0.036) and lower percentages of ethmoid sinusitis, maxillary sinusitis, paranasal sinusitis, and otitis media than patients without lung infection (8.6% vs. 30.6%, P=0.02). The Cryptococcus neoformans isolates were sensitive to itraconazole, voriconazole, fluconazole, and amphotericin B but resistant to flucytosine. Patients with lung infection had higher mortality at discharge compared with patients without lung infection (8.6% vs. 0, P=0.12). Multivariable analyses showed that WBC counts ˂20×106/L was significantly associated with treatment outcome (OR=0.01, 95% CI=0-0.833, P=0.041).Conclusions There were significant discrepancies in clinical features between CM patients with and without lung infection. Clinicians must consider the divergences in the diagnosis of CM in patients with lung infection.