Many children on the autism spectrum have difficulty developing reading comprehension skills. This multiple phase single case design pilot study examined the impact of a computer-assisted reading tool, Reading Eggspress™, with or without teacher directed instruction on the reading comprehension skills of four children on the autism spectrum (mean age 9 years, 10 months). Participants engaged in two randomised intervention phases, each lasting four weeks. Phase A involved Reading Eggspress™ plus teacher directed instruction of graphic organiser use and Phase B involved Reading Eggspress™ alone. Two participants made significant gains on a standardised measure of reading at post-test. Three participants made gains in median reading comprehension probe scores. Both phases appeared equally supportive of reading comprehension. Participants learned to use graphic organisers to support their comprehension during the intervention. Social validity questionnaires completed by parents, teachers and the participants indicated high acceptability of the intervention package.