The inability of many English second-language (ESL) learners to read at desirable levels is universal, but reasons for this and solutions have not yet been addressed. Within the South African teaching context especially there is a paucity of evidence-based research findings available on the literacy challenges faced by ESL learners and the application of effective intervention strategies. This paper investigates whether the reading and reading-related skills of ESL learners in post-apartheid South Africa can improve significantly following evidence-based direct instruction and reading scaffolding techniques to enhance reading comprehension. The paper is based on an experimental/control study of 288 ESL learners from 24 primary schools in the Free State province. Learners received small-group instruction, which included evidence-based direct instruction reading that explicitly targeted skills such as phonological/phonemic awareness, sight words and word identification, reading fluency, vocabulary knowledge, syntactic awareness, and the application of reading comprehension skills. ESL learners in the control group followed the prescribed reading instruction programme in the specific school, which entailed ESL classroom intervention using balanced literacy instruction with a focus on word study, group and individual story reading, and writing activities, without explicit instruction or reading scaffolding. Results showed statistically significant differences, with medium effect sizes, favouring ESL learners in the experimental group, thus increasing confidence that direct instructional procedures in combination with reading scaffolding techniques can boost important literacy and functional academic skills of ESL learners. Results from this study have already made a significant contribution to the hitherto scarce empirically validated research into the literacy challenges facing ESL learners in South Africa, and so are intended to open up for debate a topic of critical importance to the country’s education system.