Studying anxiety in neurogenetic syndromes may inform the intersection of biological and developmental risks, facilitating effective and targeted interventions. We longitudinally examined stranger fear in infants and toddlers with fragile X syndrome (FXS; n = 46) and typical controls (n = 33), as well as associations between observed stranger fear and rating scales of anxiety, withdrawal and autism features within FXS. Results indicated atypical facial fear in FXS, although facial fear did not index anxiety, autistic symptoms or social withdrawal. Instead, lower withdrawal was associated with decreased distress vocalizations across age, and higher autistic symptoms were associated with lower intensity escape behaviors. Early stranger fear in FXS reflects both typical and atypical dimensions and may help index emergence of social anxiety in this population.