Working memory training (WMT) for children has received great attention in recent scientific investigations. However, evidence on program efficacy is still sparse. This study aimed to investigate the effect of a WMT software program ("Programa de Ativação da Memória de Trabalho" [PRAMEMT]) in promoting gains on cognitive and school related abilities. To investigate its effect, 78 school children attending 1st to 5th grades (52.6% girls; mean age = 7.87 years; SD = 1.44) were randomly allocated to a control (n = 37) or an experimental (n = 41) group. The children participated in five intervention sessions. The control group answered questions related to the same animals and themes featured in the PRAMEMT, but unrelated to working memory. The results suggested that there were gains in the performance intelligence quotient (p < 0.05; d = -0.54) and phonological awareness (p < 0.05; d = -0.52) in the experimental group; however, there was no change in overall cognitive performance. Possible mechanisms for these findings are discussed.