Globally, gender differences are reported in the early acquisition of reading and mathematics as girls tend to outperform boys in reading, whereas boys tend to outperform girls in mathematics. This can have long-term impact resulting in an under-representation of girls in Science, Technology, Engineering and Mathematics subjects. Recent research suggests that sociocultural factors account for differences across genders in the acquisition of these foundational skills. In this study, we investigated whether a new technology-based intervention, that included activities accessible to both boys and girls, can reduce gender differences from emerging during the early primary school years. The novel instructional method used in this study employed apps developed by onebillion© delivered individually through touch-screen tablets. Over a series of experiments conducted in Malawi, a low-income country in sub-Sahara Africa, we found that when children were exposed to standard pedagogical practice typical gender differences emerged over the first grade (Experiment 1). In contrast, boys and girls learnt equally well with the new interactive apps designed to support the learning of mathematics (Experiment 2) and reading (Experiment 3). When implemented at the start of primary education, before significant gender discrepancies become established, this novel technology-based intervention can prevent significant gender effects for mathematics. These results demonstrate that different instructional practices influence the emergence of gender disparities in early mathematics. Digital interventions can mitigate gender differences in countries where standard pedagogical instruction typically hinders girls from acquiring early mathematical skills at the same rate as boys.