Children with Down syndrome (DS) using intensive computer-based phonics (GraphoGame, GG) were studied. The children's independence and improvement in phonological processing, letter knowledge, word decoding, and reading strategies were investigated. Seventeen children (5-16 years) with DS participated in a crossover design through 8 weeks (one period), with three test sessions separated by 4 weeks. Children were randomly assigned to GG intervention or regular schooling (RS). All children completed one period and eight children completed two periods. A majority gradually became independent in managing GG. At the group level, very little benefit was found from working with GG. At the individual level, several children with mild to severe intellectual disabilities showed increased decoding of trained words. After one period of GG and RS, an increase in alphabetically decoded words was found. The finding suggests that when individual challenges are considered, computer-based phonics may be beneficial for children with DS in their educational setting.