Aspiration pneumonia is a serious condition resulting from swallowing dysfunction. However, predicting high risk patients remains challenging. This study aimed to assess the incidence and risk factors for pneumonia in oropharyngeal dysphagia patients exhibiting episodes of penetration or aspiration during fiberoptic endoscopic swallowing evaluation (FEES). A retrospective analysis was performed on patients who visited a dysphagia clinic between 2016 and 2022, and demonstrated at least one episode of penetration or aspiration during the FEES (Penetration Aspiration Scale [PAS] score ≥ 3). Data collected included demographics, comorbidities and FEES findings. Outcomes included mortality, hospital admissions to treat pneumonia events, and incidents of pneumonia managed by primary care providers or outpatient medical facilities. Statistical analyses included descriptive statistics, chi-squared tests, t-tests, logistic regression and Kaplan-Meier survival analysis. Among 73 patients (mean follow-up: 3.87 ± 1.5 years), 33 (45.2%) exhibited penetration, and 40 (54.8%) aspiration. Pneumonia developed in 41 patients (56%), with 33 (45%) hospitalized. A total of 28 patients (38.4%) died during follow-up. A history of prior pneumonia (OR: 1.374, p = 0.02) and Murray Secretion Scale score (OR: 1.121, p = 0.022) were associated with subsequent pneumonia events. Reduced laryngeal sensation showed a near-significant trend toward association with pneumonia-related hospitalizations in the penetration group (58.3% vs. 19%, P = 0.052). No significant association was found between PAS and pneumonia or mortality. Prior pneumonia and secretions accumulation during FEES significantly predict pneumonia in patients presenting with penetration-aspiration during FEES. Reduced laryngeal sensation showed a nearly-significant trend toward pneumonia-related hospitalizations.