Links between temperament and social–emotional difficulties are well-established in normative child development but remain poorly characterized in autism. We sought to characterize distinct temperament subgroups and their associations with concurrent internalizing and externalizing symptoms in a sample of 103 infants (Mage = 12.39 months, SD = 1.97; 68% male) showing early signs of autism. Latent profile analysis was used to identify subgroups of infants with distinct temperament trait configurations on the Infant Behavior Questionnaire-Revised. Derived subgroups were then compared in terms of internalizing and externalizing symptoms on the Infant–Toddler Social and Emotional Assessment. Three distinct temperament subgroups were identified: (a) inhibited/low positive (n = 22), characterized by low Smiling and Laughter, low High-Intensity Pleasure, low Vocal Reactivity, and low Approach; (b) active/negative reactive (n = 23), characterized by high Activity Level, high Distress to Limitations, high Sadness, high Fear, and low Falling Reactivity; and (c) well-regulated (n = 51), characterized by high Cuddliness, high Soothability, and high Low-Intensity Pleasure. There were no differences in infant sex ratio, mean age or developmental/cognitive ability. Inhibited/low-positive infants had significantly more behavioral autism signs than active/negative reactive and well-regulated infants, who did not differ. Inhibited/low-positive and active/negative reactive infants had higher internalizing symptoms, relative to well-regulated infants, and active/negative reactive infants also had higher externalizing symptoms. These findings align closely with those garnered in the context of normative child development, and point to child temperament as a putative target for internalizing and externalizing interventions. Lay Summary: This study explored whether infants with early signs of autism could be grouped according to temperament characteristics (i.e., emotional, behavioral, and attentional traits). Three subgroups were identified that differed with respect to emotional and behavioral difficulties. Specifically, “inhibited/low-positive” infants had high emotional difficulties, “active/negative reactive” infants had high emotional and behavioral difficulties, while “well-regulated” infants had the lowest difficulties.