Background: A new coronavirus, SARS-CoV-2, was associated with a newly identified respiratory syndrome, COVID-19 in Wuhan, China, in early December 2019. SARS-CoV-2 rapidly spread across the globe, imposing increased working hours and workloads for healthcare workers. We have evaluated the prevalence of mental health outcomes and associated factors in house staff physicians in Panama. Methods: A cross-sectional study was undertaken from July 23, 2020, to August 13, 2020. Snowball sampling was used to recruit participants. Then, an electronic questionnaire with scales to evaluate anxiety disorders (GAD-7), depression (PHQ-9) and post-traumatic stress (IES-R) was administered. In addition, socio-demographic variables, clinical history of mental disorders and COVID-19 exposure were evaluated. Independent analyses for each mental health outcome were undertaken using a logistic regression analysis. Results: A total of 517/1,205 (42.9%) interns and residents were recruited nationwide. The overall prevalence of depression symptoms was 25.3%, 13.7% for anxiety and 12.2% for post-traumatic stress. At least 9.3% participants reported having suicidal ideation. The most parsimonious model showed females had a higher prevalence of mental health disorders across results, and married participants were more likely to present depression (OR, 1.73; 95% CI, 1.03-2.91; P = 0.039) or at least one mental health disorder (OR, 1.66; 95% CI, 1.03-2.68; P = 0.039). Conclusions: A high prevalence of mental health disorders was found, showing the need to mitigate this emotional burden among healthcare workers in the current context of the COVID-19 pandemic.