Background Prior research suggests that 60–74% of males and 16–45% of females with fragile X syndrome (FXS) meet criteria for autism spectrum disorder (ASD) in research settings. However, relatively little is known about the rates of clinical diagnoses in FXS and whether such diagnoses are consistent with those performed in a research setting using gold standard diagnostic tools. Method This study explored whether boys and girls with FXS met criteria for ASD in a research setting using the Autism Diagnostic Observation Schedule (ADOS) and the Autism Diagnostic Interview‐Revised (ADI‐R), and then compared these data with the frequency of parent‐reported clinical diagnoses. We also examined child and family characteristics as potential diagnostic predictors across settings. Participants included 35 females and 51 males with FXS (mean age: 10 years), who were from Eastern and Midwestern regions of the USA. Results About half of the children met criteria for ASD on either the ADOS or ADI‐R, with ASD occurring three times more frequently in males than females (∼75% vs. ∼25%). In contrast, ∼25% of participants of both genders had received a clinical diagnosis of ASD. While cognitive and language skills predicted diagnostic outcome on the ADOS and ADI‐R, these skills did not predict clinical diagnoses. Executive functions predicted clinical diagnoses, but not diagnoses per the ADOS or ADI‐R. Conclusions ASD in FXS may be under‐diagnosed in clinical/educational settings, which raises questions regarding access to ASD‐related services.