Human trafficking is a significant and growing public health concern. Subgroups of adolescents and young adults are particularly vulnerable to human trafficking, especially youth who are unstably housed or homeless. While youth experiencing trafficking come into contact with the healthcare system, they are often not identified during routine assessment due to lack of specific inquiry and low disclosure. Therefore, we utilized a mixed-methods study design to assess the differences in the identification of human trafficking among youth experiencing homelessness (n = 129) between a standard psychosocial assessment tool and a human trafficking specific assessment tool. Findings indicate that the tool developed to specifically assess for human trafficking was more likely to identify youth experiencing sexual and labor exploitation, as well as the risk factors for human trafficking. Secondly, youth reported that mistrust of the system, fear of involving the police if reported, not wanting to interact with the mental healthcare system, and stigma are barriers to disclosing human trafficking. In conclusion, healthcare providers caring for youth experiencing homelessness should adopt improved screening tools for human trafficking to reduce the risk of missed opportunities for prevention and treatment among this high-risk population of youth.