Mathematical ability is dependent on specific mathematical training but also associated with a range of cognitive factors, including working memory (WM) capacity. Previous studies have shown that WM training leads to improvement in non-trained WM tasks, but the results regarding transfer to mathematics are inconclusive. In the present study, 176 children with WM deficits, aged 7–15 years performed 5 weeks of WM training. During the training period, they were assessed five times with a test of complex WM (the Odd One Out), a test of remembering and following instructions and a test of arithmetic. The improvements were compared to the performance of a control group of 304 typically developing children aged 7–15 years who performed the same transfer tasks at the same time intervals, but without training. The training group improved significantly more than the control group on all three transfer tests (all p < 0.0001), after correction for baseline performance, age and sex. The effect size for mathematics was small and the effect sizes for the WM tasks were moderate to large. The transfer increased linearly with the amount of training time and correlated with the amount of improvement on the trained tasks. These results confirm previous findings of training-induced improvements in non-trained WM tasks including the ability to follow instructions, but extend previous findings by showing improvements also for arithmetic. This is encouraging regarding the potential role of cognitive training for education, but it is desirable to find paradigms that would enhance the effect of the training on mathematics. One of the future challenges for studying training effects is combining large sample sizes with high quality and compliance, to detect relevant but smaller effects of cognitive training.