Background Fragile X syndrome (FXS) is an x‐linked genetic disorder that represents the most common hereditary cause of Intellectual Disability (ID). Very specific behavioural features (e.g. attention deficit hyperactivity disorder and stereotyped behaviour) are associated with FXS in adolescents and adults, yet research on temperament and behavioural characteristics in young children with FXS has been more limited and less conclusive. Method This study investigated temperament differences in young boys (3–7 years old) with FXS (N = 26) recruited from a national FXS centre and controls (N = 26) matched on age, gender and race. Results Compared with controls, boys with FXS exhibited less overall surgency/extraversion and effortful control. Boys with FXS also displayed significantly greater activity and shyness and less attentional focusing, inhibitory control, soothability and high intensity pleasure (tendency to enjoy intense/complex activities), relative to comparison children. A significant interaction between age and diagnosis (FXS or control) was observed for negative affectivity only. Conclusions Attention difficulties commonly found in adolescents and adults with FXS appear to also be characteristic of young boys with FXS, as reflected by lower effortful control. Age‐related findings concerning negative affectivity may be particularly significant, leading to improved intervention/preventative efforts.