Stenotrophomonas maltophilia, an environmental aerobic non-fermentative Gram-negative bacilli, has gained attention in many nosocomial outbreaks. COVID-19 patients in intensive care unit have extended hospital stay and are severely immunosuppressed. This study aimed to determine the prevalence and risk factors of S.maltophilia pneumonia in critical COVID-19 patients. A total of 123 COVID-19 patients in ICU admitted between March 2020 and March 2021 were identified from the authors’ institutional database and assessed for nosocomial pneumonia. Demographic data and factors predisposing to S. maltophilia pneumonia were collected and analyzed. The mean age was 66 ± 13 years and 74% were males. Median APACHE and SOFA scores were 13 (IQR = 8–19) and 4 (3–6), respectively. The Median NEWS2 score was 6 (Q1 = 5; Q3 = 8). The Median ICU stay was 12 (Q1 = 7; Q3 = 22) days. S. maltophilia was found in 16.3% of pneumonia patients, leading to a lengthier hospital stay (34 vs. 20 days; p < 0.001). Risk factors for S. maltophilia pneumonia included previous treatment with meropenem (p < 0.01), thrombopenia (p = 0.034), endotracheal intubation (p < 0.001), foley catheter (p = 0.009) and central venous catheter insertion (p = 0.016). S.maltophilia nosocomial pneumonia is frequent in critical COVID-19 patients. Many significant risk factors should be addressed to reduce its prevalence and negative impact on outcomes.