The purpose of this work was to meta-analyze empirical evidence about the effectiveness of digital-based interventions for students with mathematical learning difficulties. Furthermore, we investigated whether the school level of the participants and the software instructional approach were decisive modulated factors. A systematic search of randomized controlled studies published between 2003 and 2019 was conducted. A total of 15 studies with 1073 participants met the study selection criterion. A random effects meta-analysis indicated that digital-based interventions generally improved mathematical performance (mean ES = 0.55), though there was a significant heterogeneity across studies. There was no evidence that videogames offer additional advantages with respect to digital-based drilling and tutoring approaches. Moreover, effect size was not moderated when interventions were delivered in primary school or in preschool.