Background and Objectives: Presenteeism, when employees continue to work despite being sick, may have increased among intern physicians during the COVID-19 pandemic due to the necessity of performing unfamiliar tasks. This study aimed to investigate the prevalence of presenteeism among intern physicians (IPs) in Thailand, its associated factors, and outcomes. Material and Methods: A total of 254 IPs participated in this cross-sectional study conducted from June to July 2022. Participants completed a nationwide online questionnaire including demographics, financial status, underlying diseases, hospital location and affiliation, department, resource problems, manpower shortage, workload intensity, presenteeism, and its outcomes. IPs were recruited via various social media platforms. Statistical analysis was performed using multivariable zero-inflated Poisson regression and multivariable linear regression. Results: The average age of IPs was 25.5 years (SD 1.9), and 57.5% were female. The majority of IPs reported dealing with resource problems (74.8%), insufficient manpower (94.9%), and intense workload (83.5%). Presenteeism was prevalent among 63.8% of IPs, with the most common of the diseases being allergic rhinitis (31.3%). IPs with underlying diseases had an increased rate of presenteeism (adjusted odds ratio (aOR) 2.50, 95% confidence interval (CI) 1.33-4.55). IPs working in community hospitals during their rotations exhibited a lower rate of presenteeism (aOR 0.39, 95% CI 0.16-0.94) compared to other departments within general or regional hospitals. The IPs frequently exposed to insufficient manpower had an increased rate of presenteeism (aOR 4.35, 95% CI 1.02-20.00) compared to those not exposed. Additionally, IPs with presenteeism had more exhaustion (β 1.40, 95% CI 0.33 to 2.46), lower perceived well-being (β -0.65, 95% CI -1.26 to -0.03), and job satisfaction (β -0.33, 95% CI -0.63 to -0.03). Conclusions: During COVID-19, intern physicians in Thailand often exhibit presenteeism due to physical conditions, resource scarcity, and personnel shortages, impacting exhaustion, well-being, and job satisfaction. Recommendations include assessing healthcare workforces, allocating resources more effectively, enforcing policies to promote responsible use of sick leave, and implementing sick leave systems.