Background: The Canadian fetal alcohol spectrum disorder (FASD) diagnostic guideline provides clinicians with the process and procedure to reach an accurate diagnosis. However, organisational structure, culture, and resource utilisation vary. The objectives of this study were to identify the key challenges and strengths of successful FASD diagnostic clinics. Method: Qualitative interviews were conducted with 12 key informants from 10 clinics representing different regions, populations served, and clinic structures. Data analysis was performed using iterative thematic inquiry. Results: Three themes related to challenges and four themes related to strengths were identified. Human resources were identified as both a challenge and strength. Additional challenges were diagnostic capacity and system level support. Additional strengths were clinic adaptability, relational connections, and culturally responsive approaches. Conclusions: FASD clinics are more alike than not in their approach to assessment and diagnosis. Some clinics are facing similar challenges that others have overcome, supporting the need for mentorship and consistent operating standards.