To explore associations between autism traits and family functioning over time, we studied longitudinal data of a mixed group of 168 clinically referred autistic and non-autistic children. Cross-lagged models showed a significant association between fewer autism traits at the diagnostic assessment and better family functioning 1 year later for the whole group, independently of children's internalizing or externalizing behavior. When splitting the group into autistic children (58%) and non-autistic children (42%) based on an autism diagnosis, this association was only significant in the subgroup of non-autistic children with autism traits. We hypothesized that the needs of families experiencing difficulty understanding and adjusting to their children with autism traits, but no clinical autism diagnosis, might be unmet without the training or support facilities offered to families with autistic children. Although further research is needed to explore this association, clinicians may also consider supporting families of non-autistic children with autism traits to prevent family functioning problems. 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.