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Randomized controlled trials (RCTs) are the gold standard for evaluating interventions, but they present unique challenges for research staff, particularly in substance use research. This study explores the emotional and ethical burdens faced by staff working in pragmatic RCTs involving people who use drugs. Semi-structured interviews were conducted with 36 research staff from academic medical and community-based treatment settings across the U.S. Thematic analysis revealed key challenges, including emotional strain from secondhand trauma, burnout due to overwork and high turnover, and powerlessness within academic research hierarchies. Some staff felt unsupported in addressing the complex needs of PWUD, contributing to moral distress. These findings highlight the emotional toll of working with marginalized populations and the systemic issues within clinical research settings, emphasizing the need for greater support and ethical consideration for research staff in substance use RCTs.