Little is known about family functioning over time when raising a child with autism traits, with or without a clinical autism diagnosis. Therefore, we asked caregivers-mostly parents-of a group of 168 children about the family functioning and the child's emotional and behavioral characteristics, as well as autistic traits, twice with about 1 year in between. For numerous reasons, the children were referred to youth mental health care centers, including child and adolescent psychiatric services. Care as usual was offered after the diagnostic assessment if a clinical diagnosis was the assessment outcome. Caregivers reported less problematic family functioning in children with fewer autism traits over time. The child's additional emotional or behavioral characteristics did not seem to influence this relation. Furthermore, we split the whole group into autistic children with a clinical autism diagnosis (58%) and non-autistic children with autism traits but without a clinical diagnosis (42%) to see whether we would find the same results in both groups. Surprisingly, the relation between family functioning and the level of a child's autism traits only held for the subgroup of non-autistic children with autism traits. Thus, raising children with autism traits without a clinical diagnosis may affect family functioning over time. We think that families might have difficulty understanding and adjusting to the autism traits of their children but are lacking the support that is exclusively offered to families of children with a clinical autism diagnosis. We must be cautious because we do not know whether there is a causal relation. Although further research is needed to explore and learn to understand this result, clinicians might consider offering support to families of children with subthreshold autism to prevent problems in family functioning. Because high autism trait levels in non-autistic children may be of a different origin than autism, for example, other neurodevelopmental or mental health problems, family training or support should be tailored to the child's underlying difficulties.