Implementation of evidence-based practices for autistic students must be informed by robust research literature. Randomized-controlled trials (RCTs) are often considered a "gold standard" methodology for determining the effectiveness of interventions. However, the complex nature of schools presents challenges for implementing successful RCTs. We review common challenges that researchers may face when implementing RCTs of interventions for autistic students in school settings. Additionally, we provide recommendations to researchers for avoiding and addressing such challenges, based on our own experience conducting a school-based RCT. Limitations and directions for future research are also discussed.