Background: Most people believe that student–athletes experience fewer difficulties related to mental health than non-sport participants. However, several studies have shown high depression levels or emotional difficulties in adolescent athletes. Most secondary school students have access to athletic trainers in their schools. Secondary school athletic trainers (SSATs) are medical professionals who can provide health care for student–athletes, and they could be appropriate supporters in providing mental health management in secondary schools. However, there are no studies that have addressed their preparedness and confidence level to manage potential risk factors and mental health disorders. This study aims to ascertain preparedness and confidence levels from SSATs’ perspectives in handling mental health disorders using a survey based on the mental health management guidelines and consensus statement. Methods: This is a cross-sectional study design. The research team created an online survey questionnaire based on the National Athletic Trainers’ Association (NATA) Mental Health Guidelines for Secondary School and Interassociation Recommendation: A Consensus Statement. Utilizing the NATA Research Survey Service, the online survey was emailed to SSATs who self-categorized as secondary school athletic trainers in the NATA membership system. (n = 171, 65% completion rate). SPSS was used to analyze the survey data. Result: This study found that 29.2% of SSATs reported they have policies or guidelines regarding mental health disorders management for minors. The most frequent policy was mandatory reporting in cases in which an individual is being abused or neglected (80.5%). The highest confidence area was aligned with the most frequent policy. The least frequent policy was considering unique stressors and triggers with student–athletes to recognize the potential mechanisms that may cause a mental illness or exacerbate an existing mental illness (58.5%). Even though the least frequent policy was not aligned with the least confidence area, it was the second lowest confidence level. This study identified significant differences between two different employment structures: school-based employment and hospital-based employment structures. Policies were more common in school-based employment than in hospital-based employment structures. Conclusion: This study demonstrated the gap between organizational and individual preparation. The majority of SSATs respondents expressed moderate to high confidence in their ability to manage mental health disorders, despite the lack of mental health policies or procedures in their secondary schools. This study recommends that SSATs create guidelines or procedures in the areas where they are least confident and prepared to offer mental health management for minor student–athletes. They can use the interassociation recommendations and the NATA guidelines for mental health care to close the gap.