Many children fail to acquire basic reading skills. The current evidence base for supplementary reading instruction indicates that explicit, systematic and intensive instruction in the early years for children considered to be ‘at-risk’ of reading difficulties can have significant and preventative effects on reading skills. However, little research has investigated the effects of supplementary instruction for beginning readers as they first encounter formal reading instruction, regardless of whether they are considered ‘at-risk’. The current study investigated whether using an online reading programme (Headsprout® Early Reading; HER) as supplementary instruction for readers in Year 2 regardless of initial reading problems leads to improvements in reading skills as compared to children not receiving this additional instruction. Fifty-one children in Y2 (6–7 years) from two mainstream schools in North Wales participated in the study. Participants were randomly allocated to either the HER group or a waiting list control group. Following pretest reading assessments, the HER group enrolled in the programme as supplementary instruction for up to 45 min daily for 8 months. There were significant and marginally significant differences in favour of the HER group across measures of reading accuracy and word recognition skills, with medium and large effect sizes on most measures. The results indicate that using HER as supplementary reading instruction for beginning readers in Year 2 can have a significant effect on reading skills. Further research is required to investigate the potential benefits of class-wide implementation as standard provision for beginning readers