Introduction: Flexible bronchoscopy and its new methods have revolutionized the era of the diagnosis, staging, and restaging of lung cancer. A rare late complication is post-bronchoscopy respiratory infection, but it is critical due to treatment delays, treatment cancellation, and death. The aim of this study is to identify risk factors for respiratory tract infection after bronchoscopy in patients with lung cancer. Methods: A retrospective single-center observational study of 182 hospitalized patients was conducted at U.G.H. “ATTIKON” who underwent bronchoscopy for diagnosis/staging/restaging of lung cancer from January 2022 to April 2023. Patients were divided into two groups based on whether or not they developed post-bronchoscopy respiratory infection. Results: Analyzing the data between the groups, several potential risk factors for infection were identified, including recent hospitalization for COVID-19 within the last month (OR: 6.16; p = 0.01), history of COPD (OR: 8; p = 0.03), presence of emphysema on CT scan (OR: 8; p = 0.03), endobronchial lesions causing ≥ 50% bronchial obstruction with inability to advance the bronchoscope (OR: 9.6; p < 0.01), increased white blood cell count (≥8.5 K/μL) before bronchoscopy (OR: 8; p = 0.03), and advanced stage IV non-small-cell lung cancer (OR: 9.67; p = 0.02). Conclusions: Comparing our results with previous studies on risk factors for respiratory infections after bronchoscopy, we found that recent hospitalization for SARS-CoV-2 infection was a unique finding in our study. With the increasing incidence of lung cancer worldwide and the critical role of bronchoscopy in diagnosis/staging/restaging, large multicenter studies are needed to identify these risk factors and develop strategies for early detection, treatment, and prevention.