This study compared the efficacy of the Headsprout© Early Reading (HER) program with SENCO-delivered supplementary literacy instruction. Participants were primary school children (aged 6–9) in receipt of free school meals and supplementary literacy instruction. Data were collected within their school setting. The treatment group received HER intervention, while the treatment as usual (TAU) group received SENCO-delivered intervention, inclusive of guided reading, paper-based phonics training and word recognition tasks. It was hypothesized that children in the HER intervention group would significantly outperform those in the TAU group on measures of word/non-word recognition and sentence reading over a 7-month period. Thirty-two pupils with specific literacy difficulty were randomized to either HER (n = 17) or TAU (n = 15). Literacy skills were assessed using the Phonics and Early Reading Assessment pre- and post-intervention. ANOVA and t test analysis found that HER made significantly greater gains on measures of word/non-word recognition [t(30) = 7.55, p