This randomized controlled study evaluated a computer-based intervention on emotion understanding in 32 children with autism spectrum conditions with and without intellectual disability (ID) aged 7-15 years. The intervention group (n = 16) used the program for 12 h while the control group (n = 16) was not included in any intervention or training beside the usual educational curriculum. After controlling for pre-intervention scores and symptom severity, strong positive effects were observed in emotion recognition from real face photographs and pictograms, as well as in understanding situation-based emotion across both intellectual ability groups. The typical and ID intervention groups performed significantly better on all EU measures, compared to controls, at the level of feature based distant generalization.